It's the crank sensor!
Join Date: Nov 2007
Location: Central Minnesota
A TPS generally doesn't cause a single cylinder misfire. And the same for the crank sensor. This is how I would proceed if it were my XJ.
1. Swap the fuel injector from cylinder 6 into a different cylinder and see if the misfire follows.
2. Run a compression test on ALL cylinders and see where cylinder 6 sits in comparison to the others. The compression spec for the 4.0 is 120-150 with no more than a 30 psi variation between cylinders. Can't ignore the possibility of an internal engine issue. A compression gauge can be rented inexpensively from many parts stores; call around for availability.
Good luck and keep us posted!
99 Cherokee, 4.0 AW4, NP242
Past Jeeps: 49 Willys, 81 Scrambler, 88 Comanche
Without "data", all you have is an opinion!