How high should motor be on pontoon boat

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I don't know the answer to your question. To me they seem to sit lower in the water than what you see on a boat transom. I think I would check with Sun Tracker to see if they spec a long shaft or short shaft outboard.
 
Trial and error, drop an engine on and see where the anti cavitation plat sits when up on plane. It should be just at the surface of the water, or skimming the surface.
 
Pretty much all pontoons are made for a 20" shaft length. Some of the newer ones, tri-toons especially, are made for 25".

I also have mine set one hole up from the lowest setting, and it works well.
I recommend you start there.
 

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