Well its been awhile, but I finally got a good look under there. The ujoints actually look good. I can't discern free play in any of the ujoints, though there appears to be everywhere else.
There is a bit of free play in both the front and rear differentials, there is some free play between the front and rear of the the transfer case that I will assume is the chain, and the splines on the rear drive shaft have a bit of play as well. I hadn't revisited this thread and forgot to check for side to side play in the pinion shaft. I noted that the seal on the front differential is leaking a bit, but the rear is not, though that is definitely where the loudest sound is coming from. When I shift into reverse, I can really hear two clunks in quick succession.
A suppose it wouldn't hurt to replace the pinion bearings/seals in both differentials, as well as the chain in the transfer case. How difficult is the job on pulling those bearings? Is there a particular brand of bearing that is hardier than others? For ujoints I like to go with Spicer, but just have not had to replace many bearings over the years.
Any extra input or comments will be appreciated.