Rear Shackles
 

I have a 1998 Cherokee, I put a 3 inch R/C lift on it which included, Front Coil springs, bottom control arms, rear leaf springs and shocks. The coil springs had 2 inch pucks in the front which I took out when I put the new coils in. Now the rear sits a little over 2 inches higher than the front. I noticed that the rear leaf springs shackles are 6 inches long so they must of did some kind of a lift before. My question is if I go back to stock shackles which I believe is around 1.5 inches will this level the Jeep ?

the stock shackles are about that long...imo it just sounds like typical rc issues. They should hopefully settle after awhile.

Stock shackles will lower it some for sure. Better but slightly more money would be shackle relocation boxes. They are a huge boost to how your leafs perform.