keep in mind that poly will generally transmit drivetrain vibes to the your seat, pedals, tub, and steering wheel much more than rubber mounts will. i've also heard (not confirmed though) that if swap the tranny mount for poly that you should swap the motor mounts for poly as well...something about having one point more "fixed" with poly and the others rubber that causes problems???
maybe jackstand the jeep, pull rear tires, and slowly let out the clutch in 2nd or 3rd gear. look around for anything shaking abnormally. if nothing go for 4th or 5th? just make sure you chalk the front wheels very well so you don't have a gravity suprises.
Mine - '03 TJ RE4.5 coils, long arms, 4.88 gears, arb/detroit, 35" BFG KM2's, 9.5ti, skids, etc.
Hers - '01 TJ RE4.5 coils, 35" BFG's, Hs9500, HP30/8.8, 4.56 gears, skids, etc.