Does yours have a separate transmission control module by the washer tank? If so, that might the culprit.
1999 Sport, 4.0 5 Speed, 2.5" RC Lift, 1.25 body lift, MML, JKS Quicker Disconnects, Super35, 4.56 gears, Ected locker,33x10.50x15 BFG KM2's (SOLD)
2014 Rubicon,Anvil, 6 speed, Teraflex leveling kit, 285-70-17 Duratracs on 17x8.5 Level 8 Punch wheels. RBZ and PRS+ mod, Bestop High Rock rack and High Access front bumper, Smittybilt Gen2 comp winch, Bestop soft doors, Cobra 75WX.