I had this problem on my 03 Harley Ed, built with mods.......... turns out i had lots of blow by from having bad valvesprings.... a head job and comp cams springs later, its running great! another thing, the miss could be from bad coil(s), or plugs or just from a little water around the plugs, which is really annoying but a problem on mine occasionally with my aftermarket coils.... Good luck, Merle