Unable To Move Windows 7 Pro 64-bit To New Computer?

My wife has Windows 7 Pro 64-bit installed on an old clone desktop. I bought new parts and have built her a screaming new desktop PC, but when I tried to do a restore from the old to the new, it failed. I figured, okay, I am moving from an Intel dual core environment to an AMD quad core with a completely different chipset, so it's making Windows gag. I bought another copy of Windows 7 Pro 64-bit, since I am going to rebuild the old machine later, and installed it on the new PC. Now it seems I am going to have to reinstall and reconfigure every program that is on her old PC. What a drag!

She has many programs and customizations, such as Fruity Loops, the GIMP, the Sims 3, MS Office 2007, Blender, and many others. Most - not all - of the data files on the old PC are on a separate partition, and I have successfully "restored" it to the new system. However, Fruity Loops and some other programs insisted on using the C Drive's user/documents folder for all their data, and Fruity Loops even uses system folders for some of her music files! It's a buggy way to do things, but it's her favorite music creation program, so I am duty-bound to get it transferred.