Recently did a lot to refresh the engine on my 98 Civic CX, 5 speed. I've replaced all the sensors, new IACV (twice) and new motor mounts. Replaced head gasket, had head machined for flatness, etc...

Issue I'm having is sometimes, after driving the car for a several miles, it will throw a P0505 code and the car will begin jerking when pressing the gas pedal or releasing the gas pedal. If I clear the code, it acts completely normal. The time it takes for it to start acting up varies greatly. Sometimes I will drive it for 20 miles and never skips a beat, then other times it happens after only a few miles into the drive...I've checked for vacuum leaks, none that I can see even after smoke test.

Any ideas on what to check on next that results in this behavior?

 

If it showed a p0505, which is idle control system malfunction. I would double check the IACV, any vacuum leaks, throttle body cleaning?

 

I recently had something similar on my d16y8 auto. It was a mixture of 3 things. I needed new grounding wires( one on the transmission, one on the engine). The distributor cap had a hairline crack near one of the screws. AND - just for the sake of completion- the cylinders had a really small leak into the cooling system. You can diagnose a potential cooling leak by putting a no-spill radiator funnel on your radiator and watching for bubbles. I had to get my head resurfaced to fix this issue. Hope that helps.