I have a similar clunk in my TC rearend. It is being amplified by my aluminum driveshaft so that every time I get on the gas, shift or lift, it clunks. I get the noise when rocking the car too. Thought it was the u joints, but they are hard as a rock, and the driveshaft is only a couple of years old. Everything else is good too that I can tell, just put in some torque box reinforcements. Mine does feel like a popping from the housing, if I hold the driveshaft firm, and turn one wheel, I can feel it pop.
I have a friend that rebuilds rear ends and trannys, so i need to talk to him about it. But I bet it will need a rebuild since the housing has probably 180,000 miles on it by now.