If you were to wipe your C: drive and Windows installation, you may be able to use the programs on your E: drive. It all depends on how those programs were written.
Some programs were developed without the need for registry entries or configuration files that would normally be located on the C: drive. However, these tend to be the more simple programs, such as text editors. More complex programs will require these objects, however some programs will recreate them at launch if they are missing. Typically, they revert to their default settings and any customizations you made would be gone.
Unfortunately, there is no way to know which programs can operate this way, without digging through manuals, forums, SU, etc...
You could make backup images your C: and E: drives with CloneZilla and then wipe your C: drive, do a clean install and test each program. Depending on the number of applications, that could take a while. If it turned out that too many of the programs didnt not function, you could then restore your C: and E: drives. Obviously, restoring C: returns your original OS, but restoring E: would restore any settings that were changed to the E: drive.
Now as for a program to do this for you, I believe several "installer" and "uninstaller" programs are capable of tracking all the changes during a program's installation and export those settings, however since they werent used during the original installation, you are most likely out of luck.
In the future, I would suggest making several images. Install a fresh copy of Windows and update it. Then take an image. That way, you will always have a clean copy of Windows to restore to. This is much faster than installing. Then install your applications, customizations, and updates. Then take a another image. This allows you to restore to an image with your OS and applications in a "clean" state.