[Rovernet] Diagnostic help please

[LANCE LA CERTE PSY D]

1970   3500S  P6B  NADA
Background----Rebuilt engine (2,000 miles total), rebuilt Borg-Warner 35, replaced differential (lower mileage, not rebuilt), rebuilt rear brake calipers.
Car has developed a thumping which appears to be coming from the rear of the car.  At speed it disappears, but instantly returns as soon as you take your foot off the gas.  I've had the car up on the lift and with the rear end suspended and the transmission in neutral I can rotate the rear wheels by rotating the propeller shaft, i.e., nothing seems to be 'sticking'.  I also noticed the left rear caliper is not engaging (right disc is hot to touch after drive, left is cold). 
I would appreciate any help in how to diagnose this thumping (and if I'm going to need to drop the differential to address the brake caliper.  

Lance La Certe, Psy.D.
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