Pile of crap, 2001 with a persistent cyl 6 misfire

I bought this jeep late summer early fall of 2009. It had a blown transmission, and has always had a cyl 6 misfire. The scan tool will count from 0 to 255 misfires (the max) in less than 60 seconds. The misfire disappears off idle. Emissions is due, and I need to fix this to pass. These are some of the things I've done to try to fix it, I'm sure I'm forgetting some.

• Switched PCM's (swapped to a manual PCM, nothing to do with the misfire)
• Swapped #1 and #6 injector, misfire stayed on #6
• Fuel pressure never goes below 45, never above 50
• Converted to external coil pack, new coil, wires, and NGK plugs
• New cam pos sensor
• Sync'd cam pos sensor
• Compression test, all cylinders between 120-135psi
• Manually rotated #6 valves 90*
• Timing, TPS, O2 sensor, and all sensors seem to be giving reasonable readings to the PCM

Does it hot or cold, so I don't think its related to #6 running hotter than the rest of the motor

Pretty much waiting on a pass to start the 1 ton swap, I am just at a loss. I have access to a real scan tool, so if any sensor information would be useful in fixing this I can graph it and snap a pic of the screen.

Thanks

Do a running compression test. Yes it is ok to do this, just unplug the injector. At higher RPM a cracked head or improperly seating valve will show up better.

I'll give it a shot.

First thing I thought of was a bad valve... I think mongolchuck is going in the right direction.

Thats the path im heading down, I think im just going to yank the head this weekend. I have a spare one, and Im sure the headgasket is tired anyway.

Just out of curiosity did it have the miss before you did the trans? I'm not real clear on that.

I was thinking maybe the crank position sensor isn't picking up the flywheel correctly for that cylinder. Possibly from the sensor being to far away from the flexplate or the the flexplate being damaged. I know that when I changed the one in my TJ years ago that the new one had a piece of cardboad stuck to the end to set the airgap away from the flywheel correctly.

I dont know, i bought it, towed it home and swapped the trans.