Thumping Sound
Have you tried coasting (with the car moving) and shifting in to Neutral? Have you stopped the car and given gas to the engine in Park and Neutral?

To confirm, I would listen at a shift point. Drive to 20 mph or so and then shift into Low gear, keeping gas into it to maintain your speed. Your RPMs should shoot up and if the frequency of the sound doesn't change much, then you'll know it's behind the transmission.






