Hmm. I have no idea. I would expect carrier bearings as well. Could be the rearend perhaps, but those fail so rarely its ridiculous, even considering that 99.9% of DSMers take these cars to 150-200k miles and never change that fluid
But its worth checking. Not sure how you could tell its bad though. Mine is still "good" and there is a ton of backlash in it Not sure what a bad one would look like. The only thing in the tranny that could be hosed and still allow you to drive the car is the center diff. Might be worth opening it up and putting an eyeball on it. If the pieces from that get out you will lose other shafts/gears. But typically a broken CD will lock up when making tight turns, and you dont mention that.
I'm stumped, you'll just have to start ruling things out and see whats left.
Just had a thought, drain the tcase fluid. I was getting more of a grinding than a vibration when mine was letting go, but eventually it will lock up and has it has killed people. MAke sure the fluid isnt a silver soup, and check the grain plug, it should be magnetic. Thats an easy 15 minute job that will rule out one more suspect.