Misfire

I'm getting a P0304 error code and the car idles rough. A little background, the previous owner stripped the threads in #4 cylinder. The plug blew out. I limped home. Since the head was coming off to rethread, I had the valves ground, timing belt replaced, all new lifters, both coils replaced, new wires, new plugs, new PCV. Now I get the MIL on but only if the car is cold. If I turn off the MIL when the engine is warm it does not come back on unless the car is turned off for3 or 4 houirs. The compression checks out 180 in #1, 2 & 3 170 in #4 (within allowed variance), the timing is good, the resistence on all injectors is within allowed parameters, the voltage at the ECM for all injectors is within allowed parameters. The car does not seem to miss except at idle. I noticed that when I was checking the timing that the timing light was showing the miss by skipping at irregular intervals. I switched the coils around but the timing lite still skips. I also tried putting the timing lite on the #2 wire and the same skip showed up. I was about to replace the injector(for $100+) but now I'm wondering if this is an ignition problem. I'm running out of things to check.(This is a 97 paseo with 120K miles)