Long story but please read all of it.
so I just turboed my stock 4.0 with 207k milage. Got it tuned by flyin ryan, wasn't completely dialed but it was enough I could do pulls up to 5 psi and drive normally.
About 300 miles into the turbo I went on a drive and did a 2nd gear pull, got to the traffic light and I felt a misfire, didnt hear any wierd noises but I had really high IATs. So went to the nearest parking lot and shut it off and started poking around in the engine bay, didnt notice anything out of the ordinary but I discovered by pulling injector plugs that cylinder 6 was the culprit. Made the descision to drive it 20 min home since I didnt notice anything bad and it did fine albeit on 5 cylinders.
So long story short I pulled the fuel rail to confirm the injectors were firing, they were and #6 didnt look any different than the other cylinders. Same with spark, new plug and grounded the boot to the engine and there was spark present. The threads looked fine so I assume there is a good ground on the plug. I didnt notice anything fouling the old one either, and compared it to the other cylinders with no concerning signs.
Went to compression test. On a cold engine it was 125 which is low, but within spec. Cylinder 2 was 135 for reference but I did not check every cylinder. Also did a leakdown test, there was a noticeable amount of air coming from the oil dipstick which scared me. However there is no smoke in the exhaust, no smoke from the oil fill cap, no signs of blow-by or poor piston rings at all except for that leakdown test. (I have a catch can and there is no excessive amounts of oil there either).
Did a wet compression test and the compression did go up about 20 psi which is a little too much for my liking but still it does not confirm low compression as the cause of a misfire, because 120 is the minimum allowable compression.
From my research, 125 psi is still enough for the cylinder to fire.
So then I took the intake manifold off and valve cover and checked the back of the valves as well as the pushrods and valve adjustment. They were fully closed and adjusted properly, slightly gunky but not enough to cause a leak because the leakdown test would've confirmed that.
So reluctantly I took the head off because the last thing I could think of was a head gasket failure since its a stock gasket. There was no oil mixing with coolant or vis versa, nor was it overheating or bubbling the coolant. Head gasket looked good and so did the head and block deck, no concerning marks or cracks in the pistons, and cylinder walls look fine for 207k miles. So my question is, what else could I be missing? Did I overlook something? I have the head back on and the engine almost buttoned up, but I noticed one of the alignment dowel ears on the intake was broken off so I am replacing the intake I have with a spare. If I still have a misfire afterwards and no signs of an improper reassembly then im not sure where else to go except maybe replace the injector and spark plug wire.

 

What if there were an intermittent connection to #6 injector?

 

I tried wiggling the wires and the connector while the engine was running, nothing happened. It wasnt very intermittent either...it would misfire every time I started it

 

Not sure I would have jumped into tearing down the top end, I think more troubleshooting was needed. Suggesting, not criticizing.

 

Yea now I realize there is probably another issue but at the time I couldnt think of anything else that could be my problem. Pulled the head for what appeared to be no reason