So it ended up being the clutch wear plate and flywheel. This is a good thing. I wasn't looking forward to having the transmission repaired or replaced. Since the problem was in the clutch, I am going to have them (the dealership) replace the messed up water pump. I figure might as well and it comes with a lifetime guarantee, and still costs less than the transmisson would have. That is the bad thing about being a do-it-yourself mechaninc. You don't get to lifetime guarantee your own work. Not that you don't know what your doing, but if something does get messed up, you still have to pay for the repairs. It still seems pretty ironic that the dealership was the easiest on my pocket book.
