Basic things I would check in the back (if the growl is coming from behind you) of the jeep, differential fluid level (check of metal shavings in the fluid as well), transfer case fluid level (also check for metal flakes) if the fluid is low or has metal in it it could be bearings in the rear axle or transfer case. Grab the drive shaft with the jeep in park and try twisting it back and fourth, also does it make a loud thud or bang when shifting in reverse, this could indicate worn u-joints. Does it get louder as you speed up or is it a constant grow? Just off the top of my head easy checks. I doubt it is the exhaust system. When they lifted the jeep up to install the new muffler (depending on the type of car lift used) the rear axle may of drooped down and caused the drive line geometry to change which would explain a u-joint growl after a muffler service. I would only suspect the brakes if the noise only occurred when you applied them unless the shop did a brake service while you were there, did they pull the tires off to look at the rear brakes?
