On my old 93 F150 with a limited slip 8.8 inch rear, I had similar symptoms. Replaced pinion seal, u-joint, until there was no denying that it was the differential. By that time it had started to whine pretty bad. The carrier bearings were shot and there was metallic contamination in the differential fluid. I had about 130,000 miles on it at the time. I am no differential expert, but the clunking could be the u-joint alone.
69 M-Code Mach 1
93 F150 4x4 daily warrior (gone but not forgotten)
2005 F150 FX4 Flareside