Ok. Let's analyze. I am thinking out loud. Basics first.
We need fuel, air, and fire.
Fuel lines replaced. Carb rebuilt 3 years ago. With ethanol mentioned, I wouldn't totally rule out the carb if it were my boat.
Air? Not sure I would think air filter if it starts right back up just fine.
Fire? Spark plugs and wires good? Once warmed up, I could see an issue here. I have heard of spark plugs which have hairline cracks barely visible to naked eye. Tough to tell with plug wires. Never hurts to replace them.
Ignition? Does it have points? I wouldn't think so given the year. I have had small engines in the 20hp range which are 2cyl engines. We have had coils go bad on a cylinder before. Sometimes they run fine at start up, but sporadically fire on one cylinder once warmed up when they are starting to go. Other times they just don't work and only fire on one cylinder. Could it be an intermittent deal where the coil is not working right once warmed up?
As stated, just thinking out loud. Not much to small engines so i am just trying to throw some things out for you to think about. Not trying to sound so simplistic, but when analyzing something I find it best to go back to the basics. I start ruling out things and narrowing down my possible problems. Hopefully it triggers something in your head you may have overlooked. As stated before, I don't know didley about marine engines. Internal combustion engines all share fuel/air/fire though.