What you have done so far really for the most part wouldn't affect how the engine would run. Probably a sensor has gone bad and causing the EFI to go faulty. You can install you recoil, it wouldn't affect running whatsoever. First I would take off the injector and clean it. It is probably a O2 sensors or somthing of the sorts. Honda has readings in there manual to test a sensor with a multimeter to test wether its bad or not. I would pull up a diagram and find the location of every sensors and check them after cleaning the injector. You should find your culprit in there. There usually is a airtemp sensor in the airbox, since your engine changes with air temp my guess is that sensor has gone bad.