are you sure you narrowed it down to which cylinder it is misfiring at?
If so, how did you do it?
did you start the engine and pull each spark plug wire one at a time?
if you didnt do it this way, try it, this will tell you exactly what cyl is misfiring, because it will not have any affect on how the engine runs.
once you figure out which cylinder it is put the end of the spark plug wire close to something that is ground, it should spark, it is not usual for a honda to lose spark on just one cylinder unless it's cap related, so you should still have spark.
now put the spark plug back where it belongs and look to your injector.
while the engine is still running wiggle the wires on the injector of the bad cylinder, if this makes a change in how the engine rund then you have found your problem, if not then try tapping the injector (lightly to medium light) with anything you can get in there, if this makes a change then you have found your problem.
Are you sure you have your spark plug wires in the correct order???
check all of that stuff then get back to me.