I should mention regarding the "clunk" issue: Back when it happened, I did do some investigating because as I said in my original post, I had just replaced the seal in one of the axles which involved opening the differential and removing the axle. I went ahead and opened the differential again and rotated the wheels to make sure everything looked good back there. Twice while rotating the wheels, they stopped and I didn't see anything amiss in the differential. Each time if I went the opposite direction just a bit (basically took the load off), the wheels rotated again fine.
So, that leads me to believe even more this missing bolt is the culprit.
