Thanks for the help, guys.
I think the thumping is a combination of the clutch and the U-joint. It hear a noise from the back end when I shift hard, but there's a remote possibility it's something in the trunk, or even an exhaust pipe...
The expense of getting the tranny rebuilt scares me. I know a new clutch is going to run $150-200 total (including labor), and the flywheel will probably be about as much, so I don't know if I can afford to get it overhauled.
I guess this is going to put a crimp in my plans to mod the motor.