Gew, you should only need to change the keys in 'HKEY_LOCAL_MACHINE \\ SOFTWARE \\ Microsoft \\ Windows \\ CurrentVersion' to reflect the changes, which can be put in a .reg file to run. I would also do a mklink /J (junction) instead of /D (directory link) as it's more stable. If you need a hand writing a .reg file, let me know.
It also works with the Users, ProgramData and Program Files (x86) folders (for 64-bit machines), though you'd need to change values in 'HKEY_LOCAL_MACHINE \\ Software \\Microsoft \\ Windows NT \\ CurrentVersion \\ ProfileList' as well if you were doing any of that. I've had this setup for over a year now, and did it again when I migrated to 7 with no problems..
Territorial, I know it's an old thread now, but as long as your Program Files directory is where the key is pointing, it shouldn't be a problem.
Hope this helps.