Are you using this same air cleaner?
http://www2.***boat.com/image_center...24IMG_2263.JPG
I would try a few runs without it, and at least gut it. I know the ones I used to have on my motor were pretty restrictive.
Also, are the plug wires the same wires you had before the motor build? If so, I would get a new set of wires, or at least test your current set to make sure they are working correctly, and even double check the plugs. So I would check the wires.
Lastly, I don't know if someone has asked this or yet, but have you checked to see if WOT on your (foot pedal or hand throttle) is truly WOT on your carb, and if your secondaries are truly opening up all the way as well.
Good Luck!
HBjet
Excellent suggestions there HBjet!
On my boat the scoop with the filter killed 200rpm vs scoop only, I've also has plug wires fail in between outings. All I could figure was pulling them off and setting them aside to take plug readings must have damaged them. Of course it ran fine the time before so I was real confused when it had a miss the next week.