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This sounds like you might have a fuel restriction in the boat side fuel system. Here is a test you can perform to verify this is an issue or not. This will tell you if you have a engine related issue or a fuel supply issue.
Get a vacuum gauge, a brass tee 3/8 and some fuel hose. Tee in the brass tee on the suction side of the fuel pump (location A,B or C) and connect the vacuum gauge. Run the boat all rpms or till the engine starts to loose power and watching the vacuum gauge. The gauge should never exceed 2" of vacuum, if it does you have a restriction in the boat side fuel system.
Check for debris in the fuel tank clogging up the screen on the end of the pick up tube, check the anti siphon valve at the top of the fuel tank, inspect all fuel lines for deterioration.
Is this engine EFI or MPI? Could I get the engine serial number please?
Still have same issue. Since I tried your solution I took boat in and had it put through complete diagnostics via computer module plug in. Every thing checked out fine and he just said bad gas. I put additive in it (seafoam) and tried again this week. It is running longer before it starts to miss and sputter. Last night we came across lake at 3200 rpm for 20 minutes then it started sputtering so I throttled back to 2600 and it ran smooth but of course it is not planned off so crappy ride back to port. What I have put new spark plug wires on and new distributor cap....could it be coil heating up and shorting out?