Clone Windows 2008 R2 to a small system drive

I am trying to upgrade a Dell PowerEdge T110 II server. It currently has 2x1TB drives. They are not configured for RAID. One is the system drive, the other is a data storage network drive.

My end goal is to put 2x4TB with RAID1 setup for the data drive, but first I would like to replace the 1TB system drive with a new 500GB drive I have.

I have been able to use Macrium Reflect to clone from the 1TB system drive to one of the 4TB drives and boot from the 4TB drive. However, when I clone to the 500GB drive, it doesn't boot, with error

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 langugae settings, and then click next
3. Click "repair your computer."

Status: 0xc000000e Info: The boot selection failed because a required device is inaccessible.

I think it may have something to do with bcd, or the BDEDrive partition's placement on the smaller drive?

bcdedit shows the new drive (500GB) holding the bootmgr and the drive I cloned from holding the boot loader.

Also, this machine is in use at a small 7 person office, I can't currently take it down or risk hurting the existing disk. I have a backup, but since I can only boot from my 4TB clone, not my 500gb clone, I have been unable to finish the configuration.

I would greatly appreciate some information on how to proceed. I also do not have any sort of rescue disk. I was not around when it was originally installed.

Thanks! Greg

Well, I finally got it to work. The steps I took were probably the wrong way to do it.

I also had to procure a Windows Server 2008 R2 disk, although Dell eventually told me I could have used the trial version.

1) I cloned the original (1tb) disk to a 4tb disk, 
2) then consolidated the free space to the beginning of the partition, 
3) then shrunk the partition to under 500gb, 
4) then cloned it to the 500gb drive, 
5) then ran startrep in the recovery command line of the 2008R2 disk.

It was very tedious.

Thanks!!!