I'm sure this won't make anyone feel better but I have a very similar issue with mine. I have the Turbo & Intercooler Setup on a 2006 TJ Rubicon 6MT w/ 49,000miles and was all original when I put the kit on. It threw a P0304 cylinder 4 misfire, about 2 weeks after install back in March 2018. Fought with it for a while back then, then had the turbo go about around a month after install. The bypass butterfly valve stuck closed, so it was boosting to 12-14psi. I don't know about you guys, but my turbo, in particular the bypass valve is very loud. You can here it modulating open and closed when you go up and down hills, even before it loads up enough to build positive boost. To me it sounds like a boost leak, but I have looked everywhere, and there is no leak.
Back to the misfire.
It has been throwing the code ever since install, it has developed an intermittent rough idle where it will die. When it does this, you can see the harmonic balancer moving a lot.
I verified engine compression, all good.
I installed the DEI fuel rail, and injector insulation, and new reflector insulation piece.
I have gotten the new tune from Banks, no difference.
Checked for vacuum leaks, no difference.
Pulled the exhaust header to turbo, verified no leaks, still have CEL.
Replaced the plugs with regular old copper plugs, no difference.
Put platinums plugs in, no difference.
Replaced coil pack, no difference.
Replaced crank sensor, no difference.
Verified crank and cam are in sync.
Put new flywheel and clutch in, (were concerned the flywheel might be warped affecting crank sensor)
We've hooked up a Snap-On scanner tool, and noticed that cylinder 4 has an intermittent misfire about 2 every 10 seconds, but when it rough idles, its cylinder 1 that completely checks out, and misfires 10-14times within about 10 seconds. If you blip the throttle it will clear itself and go back to normal idle. If you leave it alone it will die within about 10 seconds.
I have noticed that the intercooler uses some coolant. I'm not sure whether that's normal or not.
I'm starting to look down the barrel of pulling the kit back off, unless some wise sole out there has an idea I haven't thought of yet.