no offense, but u sound young & unfamiliar... we've all been there, so dont be insulted... muffler/exhaust towards the rear, wont cause the the vehicle to "shake"... physical vibrations/"rumble" at IDLE, can only be explained by engine combustion, & it'll obviously be in the front end... if it's from the rear, at idle it'll be exhaust related... could be a leak in the piping/muffler, or hangers if u hear a metal "clanging"
also might be a good idea to let it be known what year (pre-91's are renix, pre-97 are High Output 4.0L 6 Cylinder "old" body style, 97-01 are "new" body style, difference in 99-01 were re-engineered ignition & exhaust), transmission (3 different manual trans', post 91? is the most common ax-15, all automatics are aw4), transfer case (242, with all-time 4-wheel drive, 231 is part-time only), axles (all factory xj's came with the dana 30 up front... in the rear would commonly be either dana 35 or chrysler 8.25... if u have ABS, it has d35... some "old"/early models came with dana 44 in the rear)...
thats just a little important "head start" info for u... this is what u should tell us when u need engine/transmission/intake/exhaust/electrical/cooling help/info... the fact that u have a 3" lift & 31's isnt necessarily important to these areas, & especially at idle