Here are some possibilities. Troubleshooting is a process of elimination; these are suspects.
*Verify fuel pressure. Verify, but for a 99 Cherokee the spec is 49 psi, plus or minus 5 psi. Only takes a few minutes and a fuel pressure gauge can often be rented from many parts stores; call around.
*Swap the fuel injector from cylinder #1 to a different cylinder. If the misfire follows with the swap, you have found the root cause of your misfire.
*Test compression. Not as likely, but can't rule it out. The compression spec. for the 4.0 is 120-150, with no more than a 30 psi variation between cylinders.
*Test your "throttle position sensor".
99 Cherokee, 4.0 AW4, NP242
Past Jeeps: 49 Willys, 81 Scrambler, 88 Comanche
Without "data", all you have is an opinion!