I personally would start afresh and reinstall Windows 7.
But make sure before you do that you are prepared.
Like you I have an SSD and on Tuesday transferred my mobo with new RAM and new SSD to a NZXT Phantom Red case.
Like you I just have my OS and programs on the SSD with everything else on a separate drive which is is then backed up to a networked drive.
I keep a folder on that drive which has all the latest drivers and all the programs I tend to use often.
I also use Ninite click here which makes installing most of the more popular programs a doddle.
I have also gone from 32 bit to 64 bit with the extra RAM I purchased and so far everything I have installed works fine with 64 bit.