I have a 2005 f40 Yamaha that is driving me crazy. It has picked up a miss at 5900rpm and up. I can back off the throttle below 5900rpm or trim all the way down and plow water keeping the rpms under 5900 and it runs perfect. It feels like and electrical miss, not a fuel miss. It will run 6150rpm when cold but after a few miles it starts missing and I can back off the throttle and it goes away. I've drained the fuel and replaced the fuel filter. No signs of water and the fuel is fresh. The plugs are nice and brown. Timing belt is tight and in time. Runs perfect other than this hot high speed miss. Any one ever run into one doing this? Thanks in advance.
The overrev kicks in at 6200 on this motor I believe. As mentioned you are underpropped. Recommended cruising rpm is in the upper range of the motor (5k-6k). If I was rigging this motor I would prop it so that at WOT it is just hitting the rev limiter, with no gear, passengers; just a full tank of gas and you. It could be that your "miss" is valve flutter at that high of RPM.