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I recently did a SOHC VTEC swap on my 99 civic hatchback. I used all 99-00 Civic EX parts to do this (ECU, harness, manifold, etc). The car runs fine, but I continue to get misfires from time to time which obviously throws CELs. I've adjusted the timing, set the idle (it seems to sit low sometimes though. I should try setting it again)and have recently replaced the spark plug wires. It tends to throw the misfires codes out when I start it and it sits running for a little bit. Is there something I've missed that would prevent this? Thanks.
 

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also check ur injector wiring harness,

with a head swap/ head removal, installation maybe it messed up sum of the wires? happend to me once, and i thought i had a bent valve, removed the head overhaul it with new valves and still a mis fire, open'd my injector wiring harness's insulation and suddenly it stopped missing.. hahaaha

worth taking a look ,

HtH
 
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