As my signature states, I have an 00 GT 5 speed. I too, have a bad TO bearing, but I live with it until the clutch is a total gonner. It sure sounds like a defective TO to me. Heck, you have the warranty, use it! Take it back, and have them tell you the problem. Ask to ride with the mechanic if they will let you, he wants the work, he gets paid if there is a problem! Point out the issue.
I wish you luck, and keep us posted.