Looks like you checked the main culprits. Given your boats age is about 8 years, try changing the plugs, wires and cap/rotor (I assume you did the fuel filter). Had a 5.0L Mustang do as you described, due to plugs getting fouled a bit at idle. Would clear once I got some air-flow through the engine, but would get a little blocked up at idle (I could lean out the fuel to each cylinder until it would clear up with a hand-held computer).
As far as a fuel press issue, could still be (stay constant?). Pull the vac line from the fuel press regulator and see if it does the same. Try running it with your fuel cap off too.
Try an actual Volt meter, and make sure the voltage regulator is OK on the alt. I think you should normally see about 14V with a properly running alt. Maybe hook up a batt charger (10A should be plenty) and see if that makes it stop surging.
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Walt B
"Debt-Charged"Black '07 H210SS6.2L Bravo One turning a 21P HIFive
Wakeboard Tower with Perfect Pass Stargazer version
Missouri River; Kansas City, Mo.