Thats a tough one. I think it's possible that maybe one of the spark plug wires may be the culprit. Since you moved the wires one may now be arcing to another causing a misfire. I'd hate for you to buy new wires though because it could be many things. The only thing I can think of is maybe somebody will let you borrow a spark plug wire so you can try swapping it out one at a time to see if it solves the misfire, otherwise you'd be taking a chance on buying a set and that not fixing it.
Did you also change the rotor?