Yep, feeling pretty dumb!
And, the noise wasn't the transmission. I got the W56 in and it seems to work fine though I couldn't really put it through its paces as that nasty noise was still there.
I'm not sorry I swapped the trans, this W56 feels tighter than the old trans, it didn't cost a lot, and the old transfer case was definitely developing a problem at the output flange (oil leaking, flange moving on shaft) but it didn't solve the big problem.
I dropped the driveshaft and put the rear up on jackstands and could hear a clicking/knocking coming from the differential, so pulled everything all apart and found this:
DSC_1403 by
Will Baker, on Flickr
DSC_1400 by
Will Baker, on Flickr
So, now I guess I get to go looking for a good third member to swap in as I need to get this truck back on the road ASAP.
I'm hoping I can find two third members as I want to change gears and install a locker and/or tru-trac, so I could rebuild ^that^ one and one other one then just swap them both in over a weekend.
At least when this is all done i'll have a nicer transmission, new U-joints and rebuilt axles.