Alright, this problem has been kicking my rear for quite some time now (about a year). Swallowing my pride and asking for help here.
I have a 2004 4.0L SOHC with 175k on it with a misfire on cylinder 6 (P0306 Cylinder 6 Misfire, P0316 Misfire on Startup).
I've done a compression test already, average is around 110-120psi for most cylinders.
No vacuum leaks from what I can tell, I've also cleaned the maf sensor. I've replaced most of the basic things that could be culprits. New spark plugs + wires, coil pack, fuel sending unit, fuel filter, new injector, cleaned the fuel rail, camshaft position sensor, EGR valve, tested the egr purge valve too and it works great, new downstream 02 sensor.
I also have a new intake manifold gasket but I don't want to replace it unless I can confirm that that's the issue. Broken studs are the last things I need.
The misfire itself only happens when I let the truck idle or just let it pull itself with the clutch out for about 10 - 30 seconds, so within 2000 rpm is the margin for when it happens. It goes away after normally driving above 2000 rpm or if I turn it off and turn it back on. I've also watched live data and whenever it starts (with the check engine flashing and everything) Fuel trim changes.
With the misfire:
STFT B1: 0.8%
LTFT B1: 7.0%
STFT B2: 2.3%
LTFT B2: 3.1%

I don't trust the shops around here nor the dealerships to work on my vehicles but whatever this is, is obviously out of my expertise. I'm afraid it's either the PCM, or something internal like a bent valve, but wouldn't that cause low compression? Truck has never overheated either so the head should be fine. Lots of carbon buildup in that cylinder (looked in there with a camera) and nice dark oil so it's not a coolant leak.

Has anyone else had this problem or something similar? Getting desperate here, this truck is a project overlander and it's essential that I get this fixed.
Any help is appreciated!

 

Compression test yielded a 110-120 on average? While low, its still just above crossing the line. What was the compression for #6 the apparant problem cyl?

Performed a leak down test yet?

Test performed hot or cold?

Do you have access to a scope to look inside the cyl through spark plug hole?

Sounds like a mechnical issue since you replaced just about everything...

 

It is pretty low, caught me by surprise. I tested cylinder 6 first, came out to 110psi and from that I thought for sure it was low compression, then I checked 5 and 4 since they're right there and they came out around 120. Performed test at both hot and cold. Cold tested first, ran it for about 10 minutes, then tested again, same results. Hadn't thought of a leak down test, I don't have the gauges for it though. Wouldn't I get the same results as the test on the spark plug holes? And yes, I peaked in there with a little flexible camera. Lots of carbon buildup, expected that, didn't see any serrations or scratches on the walls, I could still see milling too.

 

Cheaper compression testers could show low readings across the board. Leak down tester at harbor frieght is only $90 and they say they are a little more consistant and reliable form of measuring compression. But if your confident that your tester is good and test went as planned, you could check into the intake leak testing near the #6 cyl. Propane, brake clean, etc can be used. Important to perform when engine is cold as if there is a leak, it may be more prevelant when metal/plastic parts are cold (less expansion).

 

That makes a lot of sense actually, I'm on my second tester. I borrowed one from my dad that his dad passed down to him, it was pretty old, It worked for a little until something broke inside of the canister that actually threads onto the spark plug hole, that initially read 60psi before that happened. Picked up a new one at autozone, an "OEM" one, that's the actual brand name, and now I'm getting the readings I listed. Maybe I'll end up doing a leak down test. Makes a lot of sense what you said about testing cold too.