Had a tune, ran like crap, took it off, still runs bad

[SpaceGhost01]

I mostly read on here and havent posted yet, but I have an issue I would like some light shed on so I know what I'm talking about when I go back to my tuner.
I installed long tube headers, 3" catted Y, and 3" pipe to duals out the back. All O2's are installed, but I dont know if they are all turned on to work. I had a dyno tune done and got my timing and air/fuel set really nice all across the RPM range. Looked amazing. Well I also had the guy put on a ghost cam tune so I could see what it sounded like. Well turns out I didnt like it so I had him remove it. Ever since then I have a crappy idle, but the RPM's dont fluctuate when the motor sounds like it is missing or surging. There is a little surge feeling, like the car wants to move forward just a little when it does surge, but not near as bad as when the lame ghost tune was still on. My code reader says I have no codes or misses, and after a few minutes it does say it goes into closed loop.

Ive checked all my spark plug connections for misses.

Is it possible to have a miss the computer doesnt pick up on? Maybe I have a cracked spark plug? Probably the back one on the passenger side if I had to go off my luck. Possibly cracked when the header went in, but I dont know for sure. I did have a miss when I got to the tuner, but we fixed it by messing with the wires.

The surge or miss doesnt ever completely go away after it gets warm, but it can get better.... or more smooth, but doesnt go away that I've noticed.

Can this be tune related or parts related? Maybe the timing he set it at for idle? I can push the gas at a stop light with the brake pressed and the idle doesnt get better. Only gets better after I completely begin moving.

Thanks for the input and I completely understand if this cant really be answered until I take it back to my tuner.

Oh, I also have bad crackling and popping from my exhaust at lower RPMs. I dont know if this is the loudmouth 1 I have on, or if it has to do with my timing/air/fuel at the real low RPMs.

[SpaceGhost01]

I've stumped everyone!