The Windows installation
is next. The procedure is different in the first step necessary to get this right. The drive image that you've mounted to copy Users to the Users partition and Program Files to the Program Files partition has a Windows registry that still points to the original locations on C: drive. That means that you need to make a fresh drive image of C: drive, one that has all the new registry editing.
You need to mount your fresh C: drive (with the edited registry) image and copy the contents to a drive/partition that is accessible to your USB/DVD rescue media (remember that ~100GB empty partition labeled Mount I told you about early on), because you won't be able to mount the image file from within the USB/DVD rescue disk.
Boot to the rescue USB/DVD media or whatever you decided to use as your tool to work outside of Windows (because that is absolutely necessary to be able to make these changes to the Windows installation). Navigate to the Command Prompt and launch it. The first thing you will notice is that the Prompt is X:\> and the other drive letters are different. Make a list of those drive letters. Start with C: and work your way down the alphabet. Run a dir command to see what is on that drive and you should be able to recognize what it's normal drive letter would be, then list those drive letters with the corresponding drive letters when booted normally into Windows. You have to use the ones you can see, but you also need to keep in mind where you're actually going to be when booted into Windows.
From within the Command Prompt, launch Diskpart. Type (without the quotes) "list vol" and hit enter. All your logical drive/partitions will be listed. Look for your Windows installation volume. Let's say for example that it is volume 3. Type (without the quotes) "sel vol 3" and hit enter. That volume now has focus. Type (without the quotes) "format fs=ntfs label=Windows quick" and hit enter. When that command completes, exit Diskpart, but stay in the Command window.
Now you're ready to use robocopy. The target will be your freshly formated Windows volume, and the source will be the ~100GB Mount volume you created and populated earlier with the contents of your fresh Windows installation drive image. Use the same switches as before, excluding (/xd) the Users directory. Once the copy is complete, you can reboot into Windows.
Start opening and checking programs. See what works, and whether or not anything doesn't work. If something doesn't work, first check the start menu shortcut or desktop shortcut to see if they are pointing to the correct drive. For all those programs that launch and work correctly from your new U:\Program Files partition (my letter U, yours may be different; use yours), you can safely delete their corresponding folders from C:\Program Files. If any fail to launch or are glitchy, check their registry entries and edit as necessary.
For those who have followed this instruction set and are having difficulties, contact me and I will help you. If I have glossed over some items and haven't made myself clear enough, let me know that as well, and I'll try to correct the error of my ways. On the other hand, if you have skipped some steps or blazed your own trail along the way, I probably can't help you. I would suggest restoring your original drive image(s) and start over, following the instruction set step by step.
This works for me on my hardware; I'm working from just such a slice and diced Windows setup for this tutorial. Whether it will work for you equally as well, I cannot say. Use at your own risk; I offer no guarantees, but I am willing to help to the best of my ability.