some kind of noise

i have a rearend noise that i can not figure out. while on jacks stands the car in first and tires free wheeling you can see the drive shaft almost come to a stop and then start with a clicking or popping noise at the time of the stoping. i pulled the rear cover on the rearend and found no gear teeth missing or bearing material . was told the plantaters in the trans were torn up by 2 trans rebuilders so i changed trans (th400). drove the car today and the same problem . in reverse backing up the popping came back strong enough to cause the rearend to seam to shift on its self any thoughts on this please let me know luke