It could very well be happening inside the transmission; I do not doubt it for a second. One possibility is you're hearing a hydraulic thumping, just the fluid smacking into components. Kinda like a thump tank off of a moonshine still.
The other is that it's just some play in the driveline somewhere, but I'd tag the trans as the most likely source. Either way, with the amount of work you've put into it to keep it functioning, I'd venture to say you're going to need a new/rebuilt AOD within a short amount of time.
