What kid of lift did you do? Manual tranny vs automatic? Did you drop transfer case?
Maybe a vacume leak or something? Check around the manifold for some rubber piping that may have came off loose since from memory thats where you have to shuv in a wrench to unscrew the shocks. Give us some more info on your rig..
The only time you'd have to drop the t-case is if you'd get very high speed vibrations as you're driving (this is usually right after taking off from a stop); this would be because the angle on the driveshaft is too steep as a result of the lift.
As far as the rough idle - unless something got knocked loose or screwed up during the install I really don't see how the two could be related. The only thing I could think of is perhaps some stress in the bushings on the stock components? It's a very long shot - but try loosening all the bolts on the suspension (don't remove just loosen) then retightening them to relieve any stress.
Did you put new shocks in as well? Perhaps these are stiffer and don't allow the frame to shift just that teeny bit as the engine 'bumps around' a little bit at idle.
Your motor mounts/tranny mounts should be unaffected as you did not drop the transfer case.
A forum community dedicated to Jeep Wrangler owners and enthusiasts. Come join the discussion about reviews, performance, trail riding, gear, suspension, tires, classifieds, troubleshooting, maintenance, for all JL, JT, JK, TJ, YJ, and CJ models!