My boat was running great until about 2 months ago. I would back it off the trailer, it would start and idle just fine, but when I would accelerate it would bog down and would get on plane. The first few times I went out and it would do this I could put it in neutral and try again and eventually it would start going. Once on plane it would run great. Each time I went out it seemed to get worse and eventually it got to where it wouldn't get on plane at all. After several tests I pulled the plugs and the lower port side cylinder had water in it. I pulled that head and replaced the gasket. The old one didn't have any obvious signs of leakage, except for one tiny spot it looked like water was passing through. Once I replaced the gasket it cured the water leaking into the cylinder, but the performance issue causing the bogging down is still there. About two years ago I had some other issues with it starting and I had to replace the stator, both power packs, the trigger and the voltage regulators so those items are only two years old. About 6 years ago the ECU was sent off and the driver circuits were fixed and the injectors were cleaned and calibrated.
From everything I have read this issue could be electrical or it could be fuel related. Since all of those electrical components were replaced two years ago I thought it might be fuel related so I've been looking in that direction. Is there a check valve on the pickup tube in the fuel tank that could be causing the issue or any other areas of the fuel system I should focus on? I've replaced the fuel/water separator and the spark plugs with no change so I'm looking for recommendations on where to start troubleshooting this issue.
Any advice is much appreciated.