Inconsistent misfiring
 

So, I got my car back from rewire, still running off the old ECU (need an ignition module to work with Haltech PS500), and when I got it was running excellent... For a few days. Now, I have a cylinder misfiring...

It misfires consistently in the morning when I drive to work, and then sporadically all of the rest of the time. Already replaced the plugs, and have a new COP on the way, in case one is going bad.

Current (likely, based on searching forum, oil in spark plug wells, minor oil leak, and exhaust coming through the catch can atmosphere vent... very little fluid in it, predominantly unburned fuel) known issues are new valve stem seals and valve cover gasket.

Any thoughts on what might be causing this misfire?

Still misfiring, still mostly doing it in the morning, and it is still bugging the shit out of me. Anyone?

One nice thing about a stock OBD-II ECU is that it has rather comprehensive misfire analysis built-in. I presume that the CEL must be on at this point, so pull the codes. There ought to be something in the P03xx range, which should give you a better idea of where to look.