If you are removing the TC drop, then definitely you need shorter bolts (as suggested by mrcarcrazy).
For your rough idle, check to make sure that you have plugged the IAC connector! Also check for broken wires or loose connector!
98 TJ 4.7 Stroker!!! Unichip tuner, D30/D44, 4.56, Detroit Locker in rear axle, 3.25RC SL, 1.25BL, 1MML, 33x12.50x15, Cager Softs 15x8, XRC10 winch, Rancho 9000XL shocks with wireless remote