I'd check your anti-siphon valve. It's in the fuel fitting on your tank where the fuel line attaches to. I've had numerous problems with mine on both engines. My symptoms were exactly the same as yours. Cleaning them regularly was helping for a while but the first time it happened I replaced the fuel pump and it acted up again early the next season. That's when I found a ring of varnish around the ball inside the valve. This spring it was happening on the other engine and I replaced the valve, which didn't fix the problem, yet the symptoms were the same - it turned out to be the fuel pump, which probably wore out due to both age and the extra work required to pump through the varnished check valve.
You may have noticed in your web search that there are both aluminum and brass check valve assemblies. I had an one aluminum and two brass valves (for two engines plus a generator), which is hint that they might have caused trouble for the previous owner as well. The aluminum one was the repeat offender for fouling up, and when I thought about it, the aluminum valve was on the other engine when I bought the boat, and when I took all three of them off for cleaning, I put the aluminum one on the other engine, and the problem moved to that engine. Brass seems to work best from my experience along with those I read about while researching the problem, so now all three of mine are brass.
If yours is brass, then you should be able to just clean it. If not, I would replace it with brass. Either way, your fuel pump could be weak as well. Hope this helps...
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USCG 50 Ton Master Inland/OUPV Endorsement+Towing
1998 278 Vista - Twin 4.3 GLs, Kohler 4KW Gen, AC/Heat.
1999 Yamaha Waverunner SUV
2003 Yamaha Waverunner SUV w/MR-1 HO conversion