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"The motor jumped up on plane and topped out at 5400 RPM's, but I lost 8 mph. Dropped from 45-37. "


That sounds like the hub is spinning some. 5400 rpm should be close to top rpm for this motor. And from what I have read on that combination 45 to 50 should be closer to top end. And I don't think you could change the setup enough to drop the top end that much with the same prop unless you did something really funky. That leads me to think the prop is slipping on the hub some.

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"I worked up to 2500 RPM's and while running at that speed the motor started spitting and sputtering. "

That could be a lean condition or a firing problem. Since you changed all the fuel related stuff that leads me to believe an intermittent ignition problem. THAT is where the hard part comes in. If you run it on muffs and have a something to see if if its firing right on all cylinders at different rpms ,then you can figure it's still something with the fuel.

I have something similar happening with my V4 Johnson since last time out. I have to figure it out...like you I have some mechanical aptitude and experience with mechanical things but not the training and experience a good mechanic has and all the tools . I may be headed to the shop too if I don't figure it out.