Could it be something silly as "connectoritus", the connector(s) from the ECU to the primary of the coil. I'd be breaking out an ohmmeter.

 

I had a random misfire on my 04 gto changed the spark plugs and wires, checked coil packs, compression then I replaced the passenger side o2 sensor upstream and it went away for like a week now it's back and all of my spark plugs when I checked them were black and sooty, car runs and drives like crap any ideas? And it smells of gas all the time too and mpg is down

 

I actually did retorque them all a while back, they where a bit out of torque but nothing major and sadly didn't do anything for the misfire

 

The motor is completely stock, thank you for all of your replies so far as they're greatly appreciated and greatly appreciate everyone that has replied, I think I might have to bust out the ohm meter and go to town lol, been racking my brain for a long time on this misfire that no matter what I do, it still misses on cylinder 2

 

I would take the intake manifold off and change the intake manifold gaskets first, it might have been off
previously and the gaskets not installed properly. If they are original, they are twenty years old.

What's the oil pressure when this misfire happens? Is there excessive rocker arm noise?
Low oil pressure from pick-up tube o-ring leakage and lifters with accumulated varnish could combine
to produce lifters that are not operating correctly. I don't know if this would cause a misfire, I'm just
speculating here.

 

Take the schrader valve out of the hose on your compression gauge and do a dynamic compression test(with the engine running)Disable the injector and coil for the cylinder you are testing.

Do it on a known good cylinder and the cylinder that you are having a problem with.

If it's a valve spring issue, it won't show up on a cranking compression test or leak down test.

The best way to do it is with a in cylinder pressure transducer with a scope, but a normal compression gauge will work in a pinch.

 

I would. Your biggest clue is that it's ONLY that one cylinder. Based on what you said about good cylinder pressure .... what else is unique to only a cylinder? The PCM to coil's primary and also PCM to fuel injector. Could have a "dirty" connection at a connector (oxide). Maybe start by pulling off the connector on the valve cover for the coil's and spray the connector pins down with some contact cleaner and reseat the connector ... and do the same with the injector.

 

Does it happen when it's damp? I once had a coil pack that only acted up when damp. When dry no issue.

 

Didn't see it asked

What are your compression numbers, specifically on number 2

From my experience on all sorts of low compression problems across all sorts of makes and models right around 130 ish is the lowest a cylinder will fire clean at idle.

You should have considerably more than that. If I remember right an LS1 will do right around 180
Edit: Stock LS1

 

I had a very similar issue a while back. Mine was on an LT1 and not an LS1 but was very similar in nature. On cold start up the car ran fine. Once warm, I had constant misfires on #4 that made the car run awful. We hooked it up to do some data logging after I had exhausted all of the obvious. What we found was that in open loop the issue was not there. It only occurred after the car entered into closed loop. In my situation, the issue wound up being the ECU. We replaced the computer and flashed my tune on to the new one. After that the car never misfired again.

 

This will also happen if 02 sensors are bad since they aren't read until closed loop. Believe the MAF can cause it as well. It's tricky the first time you encounter one running well then all the sudden goes bad and figuring out that the switch is when it enters closed loop. But once you realize it it makes things easier because you know to look at sensors that begin to be used in closed loop. Crazy it was a bad PCM though, those damn near never fail.

 

Thank you all again for the replies, I'm going to give it another look this weekend as it's supposed to be pretty nice out (Chicago), I'll keep you all posted as I'm going to try everything everyone has suggested, much love to you all!!

 

Try checking the coil pack plug in. Unclip it and spray each connector with brake cleaner. After it dries, put some dielectric grease on the pins and reconnect. This has happen to me two or three times over the years on various cars.