Jenn asked some excellent questions, as always.
The more we know, the easier it will be to diagnose.
Does the thumping only occur under load, or while you are decellerating, too?
Try this:
Put the rear end up on stands, and block the front wheels. Start it up, and run it gently through the gears, trying to duplicate the condition. If you can, pay attention to exactly when it happens, and when it stops.
Details my friend, details.
Take care,
~Chris