Philosophical Transmission Question...

[350SL4spd]

Burried in this post is a technical problem, but the main question is more opinion:
Car in question: 1981 380SL. 2 owner CA car, tens of thousands of dollars in receipts (including new sub frame), new very expensive paint job. 220k miles. Overall car is a very solid very babied 9/10. Engine and trans are out, engine is getting 100% rebuild.

Car clunked loudly dropping into reverse (and not as loud into drive but noticable) before the drivetrain was pulled. Flex disks are newer and definitly not the source of such a loud clunk. Diff mount is suspect and will be changed w/ the flexs. Center link was replaced last year.

My Question:
There is a slight possibility that the clunk is in the tranny (well, 50/50 btw that and the diff, really). Now w/ the damn thing out and already sitting on the shop floor, should it be eliminated as a possible suspect for this loud clunk? I would hate to put the new motor in and then have to pull the tranny again! But I am also nearing the end of my budget...
And the time is nigh for decision making!!

What would you do?