Besides following the link above, all I can says is BACK-UP before starting.
I did just what you did, in UPGRADE mode.
I have a fairly fast Intel i7-920 with my C: consuming about 50GB's. It took 3 1/2 hours to complete install!!! A clean install of course is much faster.
After install completed I had 2 new folders, saved Vista files needed for my apps and there as 'back-ups'.
Much to my surprise, I never needed them. I did find a few programs that needed re-installing, but otherwise, only one program had to be removed, DVD Flick, continual BSOD's, but I never tried a re-install to check if it would be fixed. I might have had to do some other removals, but I can't remember, I did the upgrade 6 weeks ago and have never looked back.