Ok so I upgraded to MT 3.3 and but, of course some things got changed around. Tommorrow if I have time I will work on putting some of the code back to the way it was, (javascript effects will work, modules will be added back in, etc.) So far this new upgrade, I don't notice any real changes, other then the fact that the user interface on the admin side looks a little bit different.
EDIT: Wow, I just tried using StyleCatcher and apparently it works now, SWEET.