Xj 4.0 oveheated
 

My 2000 jeep xj always ran pretty good had lots of low end torque. It had an intermittent skip on cyl 6 at idle depending on the moisture but it didnt affect the power. The temp ran around 190 - 210 on a normal day. The heater core hose started to leak a little, I didnt notice it and drove for 50 miles until I came to a stop light and noticed smoke from under the hood. It wasnt overheating but I pulled over check the tank saw it had plenty of coolant in it. I turned around and drove another 50 miles back kept an eye on the temp ran 210 the whole way. Got home put a new hose on it check the level the tank had plenty of coolant in it, so I drove it 15 miles into town and the temp guage didnt move until I turned the heater on and it shot up to 220 and back down to 210, it was blowing hot then cold then hot. I went home open the rad cap nothing came out, so I let it cool, the tank showed a good level of coolant in it, but It was almost dry, the top rad hose didnt feel like it had water in it, i open the rad cap and it took half a gallon of antifreeze. Took it for a drive and it runs a lot cooler than it did before but now it misfires all the time on cyl 6 at idle and driving and it doesnt have the low end it had before but When I floor it she lays down some rubber. Did I do damge to the motor letting it run low on coolant? Why does the resiviore show it is full but the rad be empty?

When the coolant system heats up and expands, it can send coolant into the reservoir, as well as any expanding hot air. Then when the coolant system cools it creates a vacuum that will pull coolant from the reservoir (from the bottom to avoid getting air into the system). Because of your leak, you were losing a small amount of coolant (gradually), but when the system cooled instead of pulling in coolant from the reservoir, it just pulled in air from the leak. That is why the level went down without the reservoir changing.

You most likely did not damage the engine because of this (at least not this alone). Those problems probably have their own causes.

How did you determine that you have a misfire in a particular cylinder? Have other things like plugs, coils, and fuel delivery been ruled out?

The cel comes on and off and it comes up as cyl 6 misfire and a small evap leak. I changed coil plugs and wires but nothing changed. The fuel pump is putting good pressure to the rail, might be an injector? I noticed it has some of the wire coating coming off and exposing the wire on the injector plug wire not sure if that has something to do with it.

Hell yes it does! Moisture or oil on the bare wires can cause it to misfire. One of those wires goes to the PCM and gets grounded to trigger the spray. The other is hot 12v with the engine running all the time.

Thank you for the reply, do I replace the wiring harness or can I cut and slice the wires?

I was worried I did some serious damage to the motor because it used to be a little more snappy.
is ok if I cut and slice the wires together or do have to buy a wire harness

If the conductors are undamaged I'd tape them up (using something rated for heat) or use heat shrink if you can get it on there. If you're shooting for a Concours Win then yeah, a new harness would work too :)

I'll throw some heat shrink on there, thank you