On my brothers Avalanche he had the loud pop/ clicking noise and turned out to be his u-joints. How old are your u-joints?

 

when you pulled the DS out did you make sure the needle bearing were all good to go? or did you not have to pull it?

 

I didnt pull the driveshaft.

For all I know the u-joints could be original to the truck. Alls I know, is that they weren't making any noise before I lowered the truck.

Also of note, this truck sat for a long time undriven.

 

Lowering the truck changed the operating angle of the u joints. Change the u joints, and I'll bet it cures the clunking/squeaking problems.