D16 Help! Misfiring

[civic8891]

I have a 99 ex with a 96 ex motor running off the 99 obd2b ecu. The problem is that when the motor runs, it misfirers. Sometime it runs and drives with very little misfirers and then other times it misfirers often and during acceleration. And the misfiring is random and never consistent. I have changed plugs, rotors, cap and set ignition timing. COuld running the obd2b ecu on the obd2a engine have anything to do with it? what else should I check for? Thanks

[astroboy]

Are you throwing any codes? I suspect a map sensor is at fault...I don't know the difference between the obd2a and obd2b ecu but I am thinking that is not the cause unless the sensors between the a and b are different. Also, has the car run properly since the swap?

[meat]

your ignitor in the distributor is most likely shitting the bed. also what condition are your plug wires in? this could also be a lame coil. for the hell of it make sure all your grounds are clean and tight and all your plugs and connections are on properly. my guess is a bum distributor though. new cap and rotor and plugs wont solve a faulty coil or ignitor problem though