Reassembled the engine about a week ago after the car blew a head gasket. I have the factory repair manuals, which are a wonderful resource, and I'm following them as closely as I can. I sent the head out to be refurbished since I didn't want to do that work myself, but I've done all the other work myself. I've replaced or cleaned practically everything that came off the engine during the process: New belts, water pump, radiator, thermostat, plugs, plug wires, cap, rotor, VTEC solenoid valve, knock sensor (broke it getting the head off), crank position sensor assembly, etc. I cleaned the entire intake manifold and throttle body spotlessly inside and out, and I also removed and cleaned the fuel injectors.

The engine starts without much trouble, and runs very smoothly when revved above 3000 RPM, but it runs very rough at lower RPMs and will die if dropped to idle speed. It has been consistently throwing the P301 and P303 codes (misfire on cylinders 1 and 3) and the P300 (random misfire) code. I've done tons of diagnosis, but the codes always point to those two cylinders.

It's getting spark on all cylinders, which I verified with both an inline test light and by visual inspection (plug removed and grounded, brief engine turn-over). I've swapped the plugs around between cylinders, but still the same codes.

I've also done extensive testing on the fuel injectors. All injectors are getting signal (verified with NOID light), and they are actuating when the engine is running (verified by listening with a stethoscope). I also swapped injectors 1&2 and 3&4, but the misfires stayed with cylinders 1&3. I also removed the entire fuel rail, left all injectors in the rail, turned the ignition on to ensure fuel pump had pressurized the fuel line, then applied a short burst of 12 volts to each injector and each responded with a perfect fuel spray.

I can't for the life of me figure out what else could possibly be wrong that would cause a pesky low-RPM misfire to stick with those two cylinders. Any ideas? I didn't adjust the valves when I got the head back from the shop; I assumed the shop would have done that (but perhaps a bad assumption). Could this cause such a misfire? What about the distributor coil? I haven't replaced that yet... Cylinders 1&3 are next to each other in the distributor rotation (which piques my interest), but I have spark at the plugs, so I'm not sure how it could still be an ignition problem.

I would appreciate any fresh insight; I'm running out of ideas... Thanks.

 

Yes. Check & adjust the valves. Doing a compression test before and after the valve adjustment might be enlightening.

 

Yes, a bad assumption on my part indeed. Compression test before adjusting the valves:

1 - 120
2 - 130
3 - 30
4 - 180

After adjusting the valves:

1 - 193
2 - 190
3 - 190
4 - 205

Runs like a top now. Thanks for pushing me in the right direction.