I have a 96 cherokee 4.0 it runs fine for about 40 minutes or so and then starts missing when you give it to much throttle. Changed coil wires plugs cap rotor fuel filter. Checked fuel pressure ohmed all injectors smoked tested for vacuum leaks. No codes. The only bone this thing has given me is when a mechanic put it on his scanner while it was missing and it was number six only.

 

Op temp?
It may not be a cause...but to rule it out...have you done a compression test?
When you tested the injectors... when it starts to do it... shut it off.. pull that injector, test it into a plastic bottle, fire it back up see how it's functioning. then pull that injector and swap it with one from another cylinder....then fire it back up and see if you get the same spray pattern results.
Could be injector or short in the wiring/connector?.... I didn't have that problem, but I've seen goofy things like that before, so it's easy to rule it in or out and it won't cost you any money to do it.

What I'm getting at with the test...is that if it does the same thing with a different injector that is tested and running as "good"...then it's not the #6 injector...it's further back. wiring/connector direction most likely.

 

Put a scanner with live data on it and when it runs poorly observe your TPS, map, fuel trims ,fuel system status , coolant temp, air temp. Or take a picture of all the data and post it on here. Limit your part change outs as this can make finding the issue harder.

 

I vote crank position sensor or cam position sensor

 

Do you know your vacuum? The compression per cyclinder? Fuel pressure? Gotta start with these things.

Also, yeah, check the CPS, but look inside the distributor, tug on the shaft for free-play. Look at the star under the rotor (the pick-up inside the distributor) ..I had one that corroded from age and one of the tips wasn't registering. Wasn't until I touched it and it crumbled in my hands that I figured out what the problem was.

 

Open, grease, spray with proper plastic safe silicone spray both the cam position sensor connection and the crank position connection.

 

I had a 78 bronco that ran fine until it got hot, then it would die. Turned out to be the distributor. just a thought

 

Well if the mechanic put on the scanner and it said misfire on #6, I would start by looking for a misfire on #6.

 

What plugs did you use? Going with the auto store recommendation doesn't always work. If champion make sure they are double platinum tip (platinum on both sides of tip). Single tipped can cause misfires when hot. There are other copper plugs trashy work too but what they have on file in the computer often is wrong.