If you're hearing something when shutting the engine down, it nearly has to be the TC, either attachment to, or internal of. When things fail inside the trans, it typically involves much more binding and grinding since the planetary gearsets are always fully engaged except in neutral. Have you checked that the transmission shift linkage is moving the shift lever properly? Even in neutral though, nothing would continue spinning after the engine stops.
The bolts attaching the flexplate to the torque converter may back out, but normally make a pretty distinct noise as they are beaten about by the ring gear. It is possible that they can drop without the usual clanging and grinding, so I wouldn't discard that theory before checking. If they were to all come out, and not be making noise, what you are hearing could be the TC nose spinning loose inside the guide at the back of the crankshaft, after the crank has stopped.
Inside the torque converter there is a sprag clutch that may fail, and although very uncommon, will basically render the torque converter disabled, as it can no longer direct the fluid properly between the pump and stator. (similar to the overrunning pulley on the alternator) but here, again, there would be nothing spinning down after the crankshaft has stopped.
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