I just had an idea, it could be getting stuck at the HTC screen because of the .zip files on the SDcard so I'm going to try the update one more time and if it does not work then I will remove the .zip's from the SDcard to see if removing them helps! I hope so -fingers crossed-
Edit: Nope, no difference. Ugh...wish I had never rooted in the first place.
Edit 2: I had another thought, why not try to run the .exe while the phone was showing the HTC logo, and surprise, it is now working! I really hope that it removes root, fixes the market, and gets that update!