I installed a 4.5 rough country lift on my 90 xj about 2 weeks ago and i installed full rear spring packs and I have a bad popping noise from the rear i have rechecked all the bolts and everything is as it's suppose to be and is tight but when you flex the rear it pops badly, I think it may be where the hangers bolt to the rear of the springs.

 

My first thought is u bolts are loose but you say you checked bolts and nuts. Flex it out and get someone to see if the shackles are hitting the body. I had to trim out the sheet metal behind mine for extra clearance.