I've been having this issue with my xj for about over a year now, and just replaced my Crank and Cam sensor with a Mopar unit, checked my wiring and everything checked out. But when I accelerate, I'm getting this huge CLUNK/Hesitation miss like issue with my Jeep and its driving me up a wall. The check engine light comes on instantly when it bucks for the Cam/Crank sensor with a P0340 and a P1391 even AFTER checking the forums for those codes and fixing the wiring/sensors. I'm not sure what to do but its scary as hell when you hit 40 and you feel like your motor's about to explode and you feel like you lose power then nothing happens after that but slight bursts of hesitation. I've also cleaned my throttle body and the TPS etc. I'm just not sure what to do, it's becoming pretty unsafe to drive. Any help is appreciated. When I installed my new Cam sensor I did notice a lot of play in the metal shaft that the rotor button sits on, could this be throwing the cam sensor issue perhaps, even after replacing everything else?

IAC Clean
Throttle body completely cleaned
I've unplugged O2 sensors and nothing changes (1, then plugged back in, 2, same issue with them unplugged)
Replaced Cam sensor
Replaced Crank
Replaced rotor cap, plugs, wires, button, (play in the distributor shaft?)
Fixed Wiring to cam/crank

Any suggestions would greatly help. I might have to take it somewhere to get checked out because I have no idea what I could do besides replace the entire distributor

 

I have heard of both failed distributors, and bad wiring near the connector, so I would check the 2nd, and if not, you may wish to try a new or used OEM distributor

I have a spare running XJ that is ~50 VINS away from mine, so I can, and have, replaced a failed part across from it until the new part arrives

 

Here's one for ya. According to the book, '99 Cherokees do not have a CPS, only 2000's do.

 

Not sure what book you're referring to...
All XJs have a CPS (crankshaft position sensor).

I think you're confused with a CAM sensor on the distributor (sometimes confusingly also called CPS by some). But even then your post is still incorrect - the '00 and '01 have coil packs and no (need for) distributor like the older XJs. The '99 has a distributor and therefor a CAM sensor.

 

but where is it?

 

The CPS is on the bellhousing
The CAM sensor is located in the distributor

 

Just for reference, I fixed this problem by replacing the distributor as there was just enough play in the shaft the rotor sits on to be causing issues, no matter what Cam Position Sensor I put in there. (Round plastic plate that goes under the rotor).