Start Menu, Metro apps, and other functions are broken after migrating system directories with symlinks

I've tried several times now to migrate Program Files, Program Files (x86), and AppData to my second HD with various degrees of success. (I have already migrated my User directories to the second HD with the "Location" tab in their Properties.) For the most part, everything is fine, except for a few features misbehaving;

• Searching in the start menu completely breaks
• Windows 10 "Metro" apps either open and warn that "This app can't open" or open then immediately close (MS Edge opens then immediately closes, others give an error)
• Sometimes, the Linux Subsystem for Windows (LXSS) fails to install with error 0x80070005 (some relevant issues on the GitHub page)

What I did:

1. Copied the directories I wanted to change (AppData, Program Files, and Program Files (x86) with ShadowCopy to my second HD
2. Booted into the recovery command prompt
3. Deleted the old directories with rmdir /s /q
4. Created junctions or folder symlinks with both mklink /D and mklink /J (I tried both as /d was suggested in another question here)
5. After each failed attempt to fix the Start menu and other functions, I reinstalled Windows and tried again

Again, for the most part, this procedure was very successful. Programs are successfully installed to the second HD by default, everything in AppData and its subdirectories is installed to the second HD, and my SSD has more free space than ever.

I've tried everything short of replacing all instances of the old directory paths in Regedit with the new paths, which I am hesitant to try due to countless warnings on this and other sites.

What can I do to solve my issues with the Start menu and other Windows features that are misbehaving?