Mine was clunking pretty bad before I lifted it and I put new sway bar bushings on and didn't have a problem after that. This seems to be a much louder noise. Almost popping instead of clunking. It's really bothering me though and I don't know what to do. Already spent more than I'd like to on the lift/tires and repairs lol. Still not sure why the front end sits higher
Pics would be helpful;
I believe the RR lift - like the RC lift is designed to be a leveling lift, which means it's designed to raise the front end more than the rear and level out your Commander to get rid of the factory, nose down stance.
I'm guessing your Commander is probably sitting level now - but because you aren't used to seeing it that way, you think the nose is sitting high - because it is sitting much higher now than you are accustomed to seeing.
I can tell you straight away to get your front upper differential bushing checked.
This is a known and common point of wear on both Commanders and Grand Cherokees alike and can cause the kind of clunking noise you are describing.
If your front upper differential bushing was already worn and you were hearing noise - the new sway bar bushings may have been just enough to temporarily band-aid the problem, while you still had the stock suspension/stance.
When you added the new RR lift into the equation, it was probably enough of a suspension stress/geometry change to get the front upper differential bushing to start making noise again.
I'm just speculating here, but, it sounds plausible to me.