I'm not in exactly the same position you are talking about here, but after a season of running since I got the boat, I went through a pretty thorough engine diagnostics this spring on my 225 Johnny.
We checked compression and leak-down, Fuel flow, tore apart the carbs and cleaned, synced the carbs. Turned out, I had a bad VRO/Fuel pump. It was leaking fuel back through the vacuum. We ended up going with pre-mix, a Carter fuel pump, regulator and pressure gauge. After all the tweaking She's runnin like a top. Edling is better, top end RPM and speed is better as well. We might even be seeing better fuel and oil consumption, as the plugs were black and wet most of last year. Running rich. Now they are the nice brown colour and dry.
My guess on this problem is fuel related. Your plugs are a possible indicator of what is happening. Black and wet = to much fuel and that will cut your performance. Light brown and it's too lean, that will also effect performance.
I'm a long way from an expert, but check that out and see what's happening. Also a compression and leakdown will help to incicate the condition of the cylinders, rings etc.
Good luck!
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Triad V21 - 225 Johnny HO
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