I got a call back from the Hyundai dealer today and here's whats going down....
They're going to replace the synchronizers, which is causing the grinding when I shift from 2nd to 3rd when I go above 30MPH in 2nd gear. Other than that...they tell me that they don't know what condition the flywheel is in unless they pull out the engine and take apart the tranny. Said it would cost me like $400 to do that. (for the flywheel)
I just told those @$$'es to fix only what was warrantied, b/c I don't have that kind of cash! I'm a poor mo fo with too many damn bills.
However, I will go check out some junkyards/eBay for the door panel and other small stuff I need. Thanks for the help guys!