EFI GPT Windows 7 boot-loader/manager issue and grub

My computer(asus N76VM 64 bit) with windows 7 (64 bit home professional) pre-installed got in a bad state while partitioning from a later installed Ubuntu environment. This had lead me to run testdisk and copy every seperate partition onto a backup HDD.
I managed to get it al back onto the original hard drive in a state that resembles the state before things went bad.

****I was able to boot into both operating systems before all the hassle started!****

Since "repairing" the HDD the computer still doesn't want to start windows 7. It's got Grub 1.99 installed and (hoping this would help me) rEFInd but they both don't work. I must note that Grub does display entries for both Windows 7 and Ubuntu. Ubuntu starts like it should, but when I choose for Windows the screen tells me: Invalid EFI filepath.

Another step I tried was running a Windows 7 repair cd, enter command prompt, reassign drive letters (they were C:\ for [OS] and D:\ for [DATA]) so they fitted the original state and then the following commands:
Bootrec.exe /FixMbr
Bootrec.exe /FixBoot
Bootrec.exe /ScanOs
Bootrec.exe /RebuildBcd
Rebooted
But they did not help, so I tried the following:
bootsect /nt60 c: /force /mbr
bcdboot c:\windows /s c:
Again, no sigar. So I started looking further and ran into this website which gave advice I am a bit concerned about trying, for I don't know the possible outcomes and I don't want to be loosing anything all over again.

Running boot info script gives me the following output (the order of the partitions might seem weird, I know that, but I don't think it is of any concern:

                  Boot Info Script 0.61      [1 April 2012]


============================= Boot Info Summary: ===============================

 => Grub2 (v1.99) is installed in the MBR of /dev/sda and looks at sector 
    1880670208 of the same hard drive for core.img. core.img is at this 
    location and looks for (,gpt2)/boot/grub on this drive.

sda1: __________________________________________________________________________

    File system:       vfat
    Boot sector type:  FAT32
    Boot sector info:  According to the info in the boot sector, sda1 starts 
                       at sector 0. But according to the info from fdisk, 
                       sda1 starts at sector 2048.
    Operating System:  
    Boot files:        /efi/refind/refind_x64.efi /efi/ubuntu/grubx64.efi 
                       /efi/ubuntu/shimx64.efi

sda2: __________________________________________________________________________

    File system:       ext4
    Boot sector type:  Grub2 (v1.99)
    Boot sector info:  Grub2 (v1.99) is installed in the boot sector of sda2 
                       and looks at sector 1569963600 of the same hard drive 
                       for core.img. core.img is at this location and looks 
                       for (,gpt2)/boot/grub on this drive.
    Operating System:  Ubuntu 12.04.4 LTS
    Boot files:        /boot/grub/grub.cfg /etc/fstab

sda3: __________________________________________________________________________

    File system:       ntfs
    Boot sector type:  Windows Vista/7: NTFS
    Boot sector info:  No errors found in the Boot Parameter Block.
    Operating System:  
    Boot files:        

sda4: __________________________________________________________________________

    File system:       ntfs
    Boot sector type:  Windows Vista/7: NTFS
    Boot sector info:  No errors found in the Boot Parameter Block.
    Operating System:  Windows 7
    Boot files:        /NST/menu.lst /bootmgr /Boot/BCD 
                       /Windows/System32/winload.exe

sda5: __________________________________________________________________________

    File system:       ntfs
    Boot sector type:  Windows Vista/7: NTFS
    Boot sector info:  No errors found in the Boot Parameter Block.
    Operating System:  
    Boot files:        /bootmgr /boot/bcd

sda6: __________________________________________________________________________

    File system:       swap
    Boot sector type:  -
    Boot sector info: 

sda7: __________________________________________________________________________

    File system:       BIOS Boot partition
    Boot sector type:  Grub2's core.img
    Boot sector info: 

============================ Drive/Partition Info: =============================

Drive: sda _____________________________________________________________________

Disk /dev/sda: 1000.2 GB, 1000204886016 bytes
255 heads, 63 sectors/track, 121601 cylinders, total 1953525168 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes

Partition  Boot  Start Sector    End Sector  # of Sectors  Id System

/dev/sda1                   1 1,953,525,167 1,953,525,167  ee GPT


GUID Partition Table detected.

Partition    Start Sector    End Sector  # of Sectors System
/dev/sda1           2,048       194,559       192,512 EFI System partition
/dev/sda2   1,556,162,560 1,864,286,207   308,123,648 EFI System partition
/dev/sda3   1,233,352,704 1,556,162,559   322,809,856 Data partition (Windows/Linux)
/dev/sda4         194,560 1,233,352,703 1,233,158,144 Data partition (Windows/Linux)
/dev/sda5   1,880,690,688 1,936,979,967    56,289,280 Windows Recovery Environment (Windows)
/dev/sda6   1,864,286,208 1,880,670,207    16,384,000 Swap partition (Linux)
/dev/sda7   1,880,670,208 1,880,690,687        20,480 BIOS Boot partition

"blkid" output: ________________________________________________________________

Device           UUID                                   TYPE       LABEL

/dev/sda1        E138-2A7D                              vfat       
/dev/sda2        598ab3d1-e1aa-4041-ba78-1de8c6762331   ext4       
/dev/sda3        4DFF26211F14E609                       ntfs       DATA
/dev/sda4        4A814AE3556AE075                       ntfs       OS
/dev/sda5        1B1666970F6A4336                       ntfs       Recovery
/dev/sda6        03dc7be8-7682-4219-8ab0-ae5d09caa1b1   swap       

================================ Mount points: =================================

Device           Mount_Point              Type       Options

/dev/sda1        /boot/efi                vfat       (rw)
/dev/sda2        /                        ext4       (rw,errors=remount-ro)


=========================== sda2/boot/grub/grub.cfg: ===========================

--------------------------------------------------------------------------------
#
# DO NOT EDIT THIS FILE
#
# It is automatically generated by grub-mkconfig using templates
# from /etc/grub.d and settings from /etc/default/grub
#

### BEGIN /etc/grub.d/00_header ###
if [ -s $prefix/grubenv ]; then
  set have_grubenv=true
  load_env
fi
set default="0"
if [ "${prev_saved_entry}" ]; then
  set saved_entry="${prev_saved_entry}"
  save_env saved_entry
  set prev_saved_entry=
  save_env prev_saved_entry
  set boot_once=true
fi

function savedefault {
  if [ -z "${boot_once}" ]; then
    saved_entry="${chosen}"
    save_env saved_entry
  fi
}

function recordfail {
  set recordfail=1
  if [ -n "${have_grubenv}" ]; then if [ -z "${boot_once}" ]; then save_env recordfail; fi; fi
}

function load_video {
  insmod efi_gop
  insmod efi_uga
  insmod video_bochs
  insmod video_cirrus
}

insmod part_gpt
insmod ext2
set root='(hd0,gpt2)'
search --no-floppy --fs-uuid --set=root 598ab3d1-e1aa-4041-ba78-1de8c6762331
if loadfont /usr/share/grub/unicode.pf2 ; then
  set gfxmode=auto
  load_video
  insmod gfxterm
  insmod part_gpt
  insmod ext2
  set root='(hd0,gpt2)'
  search --no-floppy --fs-uuid --set=root 598ab3d1-e1aa-4041-ba78-1de8c6762331
  set locale_dir=($root)/boot/grub/locale
  set lang=en_US
  insmod gettext
fi
terminal_output gfxterm
if [ "${recordfail}" = 1 ] ; then
  set timeout=-1
else
  set timeout=10
fi
### END /etc/grub.d/00_header ###

### BEGIN /etc/grub.d/05_debian_theme ###
set menu_color_normal=white/black
set menu_color_highlight=black/light-gray
if background_color 44,0,30; then
  clear
fi
### END /etc/grub.d/05_debian_theme ###

### BEGIN /etc/grub.d/10_linux ###
function gfxmode {
    set gfxpayload="${1}"
    if [ "${1}" = "keep" ]; then
        set vt_handoff=vt.handoff=7
    else
        set vt_handoff=
    fi
}
if [ "${recordfail}" != 1 ]; then
  if [ -e ${prefix}/gfxblacklist.txt ]; then
    if hwmatch ${prefix}/gfxblacklist.txt 3; then
      if [ ${match} = 0 ]; then
        set linux_gfx_mode=keep
      else
        set linux_gfx_mode=text
      fi
    else
      set linux_gfx_mode=text
    fi
  else
    set linux_gfx_mode=keep
  fi
else
  set linux_gfx_mode=text
fi
export linux_gfx_mode
if [ "${linux_gfx_mode}" != "text" ]; then load_video; fi
menuentry 'Ubuntu, with Linux 3.8.0-35-generic' --class ubuntu --class gnu-linux --class gnu --class os {
    recordfail
    gfxmode $linux_gfx_mode
    insmod gzio
    insmod part_gpt
    insmod ext2
    set root='(hd0,gpt2)'
    search --no-floppy --fs-uuid --set=root 598ab3d1-e1aa-4041-ba78-1de8c6762331
    linux   /boot/vmlinuz-3.8.0-35-generic root=UUID=598ab3d1-e1aa-4041-ba78-1de8c6762331 ro   quiet splash $vt_handoff
    initrd  /boot/initrd.img-3.8.0-35-generic
}
menuentry 'Ubuntu, with Linux 3.8.0-35-generic (recovery mode)' --class ubuntu --class gnu-linux --class gnu --class os {
    recordfail
    insmod gzio
    insmod part_gpt
    insmod ext2
    set root='(hd0,gpt2)'
    search --no-floppy --fs-uuid --set=root 598ab3d1-e1aa-4041-ba78-1de8c6762331
    echo    'Loading Linux 3.8.0-35-generic ...'
    linux   /boot/vmlinuz-3.8.0-35-generic root=UUID=598ab3d1-e1aa-4041-ba78-1de8c6762331 ro recovery nomodeset 
    echo    'Loading initial ramdisk ...'
    initrd  /boot/initrd.img-3.8.0-35-generic
}
submenu "Previous Linux versions" {
menuentry 'Ubuntu, with Linux 3.8.0-29-generic' --class ubuntu --class gnu-linux --class gnu --class os {
    recordfail
    gfxmode $linux_gfx_mode
    insmod gzio
    insmod part_gpt
    insmod ext2
    set root='(hd0,gpt2)'
    search --no-floppy --fs-uuid --set=root 598ab3d1-e1aa-4041-ba78-1de8c6762331
    linux   /boot/vmlinuz-3.8.0-29-generic root=UUID=598ab3d1-e1aa-4041-ba78-1de8c6762331 ro   quiet splash $vt_handoff
    initrd  /boot/initrd.img-3.8.0-29-generic
}
menuentry 'Ubuntu, with Linux 3.8.0-29-generic (recovery mode)' --class ubuntu --class gnu-linux --class gnu --class os {
    recordfail
    insmod gzio
    insmod part_gpt
    insmod ext2
    set root='(hd0,gpt2)'
    search --no-floppy --fs-uuid --set=root 598ab3d1-e1aa-4041-ba78-1de8c6762331
    echo    'Loading Linux 3.8.0-29-generic ...'
    linux   /boot/vmlinuz-3.8.0-29-generic root=UUID=598ab3d1-e1aa-4041-ba78-1de8c6762331 ro recovery nomodeset 
    echo    'Loading initial ramdisk ...'
    initrd  /boot/initrd.img-3.8.0-29-generic
}
menuentry 'Ubuntu, with Linux 3.5.0-18-generic' --class ubuntu --class gnu-linux --class gnu --class os {
    recordfail
    gfxmode $linux_gfx_mode
    insmod gzio
    insmod part_gpt
    insmod ext2
    set root='(hd0,gpt2)'
    search --no-floppy --fs-uuid --set=root 598ab3d1-e1aa-4041-ba78-1de8c6762331
    linux   /boot/vmlinuz-3.5.0-18-generic root=UUID=598ab3d1-e1aa-4041-ba78-1de8c6762331 ro   quiet splash $vt_handoff
    initrd  /boot/initrd.img-3.5.0-18-generic
}
menuentry 'Ubuntu, with Linux 3.5.0-18-generic (recovery mode)' --class ubuntu --class gnu-linux --class gnu --class os {
    recordfail
    insmod gzio
    insmod part_gpt
    insmod ext2
    set root='(hd0,gpt2)'
    search --no-floppy --fs-uuid --set=root 598ab3d1-e1aa-4041-ba78-1de8c6762331
    echo    'Loading Linux 3.5.0-18-generic ...'
    linux   /boot/vmlinuz-3.5.0-18-generic root=UUID=598ab3d1-e1aa-4041-ba78-1de8c6762331 ro recovery nomodeset 
    echo    'Loading initial ramdisk ...'
    initrd  /boot/initrd.img-3.5.0-18-generic
}
}
### END /etc/grub.d/10_linux ###

### BEGIN /etc/grub.d/20_linux_xen ###
### END /etc/grub.d/20_linux_xen ###

### BEGIN /etc/grub.d/30_os-prober ###
menuentry "Windows 7 (loader) (on /dev/sda4)" --class windows --class os {
    insmod part_gpt
    insmod ntfs
    set root='(hd0,gpt4)'
    search --no-floppy --fs-uuid --set=root 4A814AE3556AE075
    chainloader +1
}
menuentry "Windows Recovery Environment (loader) (on /dev/sda5)" --class windows --class os {
    insmod part_gpt
    insmod ntfs
    set root='(hd0,gpt5)'
    search --no-floppy --fs-uuid --set=root 1B1666970F6A4336
    drivemap -s (hd0) ${root}
    chainloader +1
}
set timeout_style=menu
if [ "${timeout}" = 0 ]; then
  set timeout=10
fi
### END /etc/grub.d/30_os-prober ###

### BEGIN /etc/grub.d/30_uefi-firmware ###
### END /etc/grub.d/30_uefi-firmware ###

### BEGIN /etc/grub.d/40_custom ###
# This file provides an easy way to add custom menu entries.  Simply type the
# menu entries you want to add after this comment.  Be careful not to change
# the 'exec tail' line above.
 menuentry "Windows 7" {
     insmod part_msdos
     insmod ntfs
     set root='(hd0,msdos4)'
     search --no-floppy --fs-uuid --set=root 4A814AE3556AE075
     chainloader +1
  }
### END /etc/grub.d/40_custom ###

### BEGIN /etc/grub.d/41_custom ###
if [ -f  $prefix/custom.cfg ]; then
  source $prefix/custom.cfg;
fi
### END /etc/grub.d/41_custom ###
--------------------------------------------------------------------------------

=============================== sda2/etc/fstab: ================================

--------------------------------------------------------------------------------
# /etc/fstab: static file system information.
#
# Use 'blkid' to print the universally unique identifier for a
# device; this may be used with UUID= as a more robust way to name devices
# that works even if disks are added and removed. See fstab(5).
#
#                
proc            /proc           proc    nodev,noexec,nosuid 0       0
tmpfs /tmp tmpfs optional,nodev,noexec,nosuid 0 0
# / was on /dev/sda2 during installation
UUID=598ab3d1-e1aa-4041-ba78-1de8c6762331 /               ext4    errors=remount-ro 0       1
# /boot/efi was on /dev/sda1 during installation
#UUID=E138-2A7D  /boot/efi       vfat    defaults        0       1
# swap was on /dev/sda3 during installation
UUID=03dc7be8-7682-4219-8ab0-ae5d09caa1b1 none            swap    sw              0       0
#/dev/sda7 none swap sw,noauto 0 0
#UUID=E138-2A7D /boot/efi   vfat    defaults    0   1
#UUID=E138-2A7D /boot/efi   vfat    defaults    0   1
UUID=E138-2A7D  /boot/efi   vfat    defaults    0   1
--------------------------------------------------------------------------------

=================== sda2: Location of files loaded by Grub: ====================

           GiB - GB             File                                 Fragment(s)

 814.208938599 = 874.250190848  boot/grub/grub.cfg                             1
 765.658302307 = 822.119342080  boot/initrd.img-3.5.0-18-generic               1
 743.588668823 = 798.422253568  boot/initrd.img-3.8.0-29-generic               2
 769.143566132 = 825.861615616  boot/initrd.img-3.8.0-35-generic               1
 765.462841034 = 821.909467136  boot/vmlinuz-3.5.0-18-generic                  2
 742.506031036 = 797.259780096  boot/vmlinuz-3.8.0-29-generic                  2
 769.006057739 = 825.713967104  boot/vmlinuz-3.8.0-35-generic                  1
 765.658302307 = 822.119342080  initrd.img                                     1
 765.658302307 = 822.119342080  initrd.img.old                                 1
 765.462841034 = 821.909467136  vmlinuz                                        2
 765.462841034 = 821.909467136  vmlinuz.old                                    2

============================== sda4/NST/menu.lst: ==============================

--------------------------------------------------------------------------------
# NeoSmart NeoGrub Bootloader Configuration File
#
# This is the NeoGrub configuration file, and should be located at C:\NST\menu.lst
# Please see the EasyBCD Documentation for information on how to create/modify entries:
# http://neosmart.net/wiki/display/EBCD/

--------------------------------------------------------------------------------

=================== sda4: Location of files loaded by Grub: ====================

           GiB - GB             File                                 Fragment(s)

            ?? = ??             NST/menu.lst                                   0

=============================== StdErr Messages: ===============================

xz: (stdin): Compressed data is corrupt
xz: (stdin): Compressed data is corrupt

Boot flag removed from the EXT4 partition. Now the next step is to get the windows partition that needs to be booted at C:\ instead of the EXT4 partition. I tried a couple of times with 'diskpart' on a windows live cd recovery environment within 'cmd'. However, at each reboot the drive letters get reassigned.

My setup from before everything went haywire

Edit:

Replaced the bootmgfw.efi file with a copy from the original OS partition. Now when booting windows 7 from rEFInd I get the following screen:

Windows failed to start. A recent hardware or software change might be the cause. To fix the problem:  

1. Insert your Windows installation disc and restart your computer.  
2. Choose your language settings, and click "Next."  
3. Click "Repair your computer."  

If you do not have this disc, contact your system administrator or computer manufacturer for assistance.  

File: \EFI\Microsoft\Boot\BCD  

Status: 0xc000000f  

Info: An error occurred while attempting to read the boot configuration data.  

EDIT 19 feb '14

---

I found on the site of Microsoft a Windows 8.1 trial iso. Downloaded it, installed in virtual machine 64-bit. Copied the iso to the virtual disk and used some instructions I found for making the USB recognized on the VM. Then with other instructions I found the way of making it EUFI boot able and it worked.

Now I'm waiting for the repair to be done. It's taking half an hour now and I don't know when it will be done. For the sake of reference I will be adding the sources of the information when/if this operation will be done

You need to understand the differences between BIOS-mode (aka CSM or legacy-mode) booting and EFI-mode (aka UEFI-mode) booting. Windows ties these boot modes quite closely to the partition table type: Windows will boot in BIOS mode if and only if the disk uses the older Master Boot Record (MBR) partition table type, and in EFI mode if and only if the disk uses the newer GUID Partition Table (GPT) partition table type. Your question title implies you're using GPT, but it's not clear that your computer originally used GPT. (Most Windows 7 systems used BIOS and MBR, although some Windows 7 systems sold in late 2011 and later used EFI and GPT.) If your original installation used BIOS/MBR, you'll need to install an EFI-mode Windows boot loader. This process is described here.

If your computer originally used EFI/GPT, you may also need to re-install the boot loader; or it could be that you've overlooked some critical detail, such as a proper re-creation of the EFI System Partition (ESP), which holds EFI boot loaders.

If you need more help, try running the Boot Info Script in Linux. This will produce a file called RESULTS.txt. Post it to a pastebin site and post the URL for the file here. That will give us more precise and detailed information about your current configuration, which may help in fixing it.

---

EDIT:

Your Boot Info Script output indicates that you don't have a Windows boot loader installed on your computer. You'll have to fix that to get Windows booting. In particular, because the disk uses GPT, you must install an EFI boot loader for Windows. Most pages that describe Windows boot repair assume a BIOS-based system, and so will be 100% useless to you. This page describes how to convert Windows from a BIOS-mode boot to EFI-mode boot, so something along those lines might work. There may be other pages that will help, too; or you can post on a Windows forum for help.

One more point, which you might want to deal with before trying to install a Windows boot loader: Your /dev/sda2 uses an ext4 filesystem, but is marked as being an EFI System Partition (ESP). This is incorrect and could cause problems down the line, so you should fix it. There are a number of ways to do this, depending on what partitioning software you use. For instance, in gdisk, you should change the type code from EF00 to 8300 by using the t option, then write the changes via the w option. In parted or GParted, you'd remove the "boot flag" (and in GParted apply the changes).