I had a misfire under hard acceleration after my 04 Rocket's engine had been removed for work at the dealer. I eventually traced it to a loose plug where they are all bundled together behind the headstock., under the front of the fuel tank. The wiring had been thrown together, one of the cables going to the handlebars had been stretched and it was enough to pull the plug slightly under acceleration. I just made sure they were all routed tidily so as not to put any stress on the plugs, made sure the plugs were connected tight and there was no pull on the cables when the bars were on full lock. End of problem. So if you, or a previous owner, has been under there and disturbed the wiring at that point, or fitted rivco risers which can pull the wiring it could be worth a look.