If the engine didn't have a big problem on the dyno, then I would believe something is not correct with the fuel delivery in your boat. Are you running the same fuel pump, Did you check your fuel pressure at idle and under load, Is your battery putting out a steady voltage same as dyno's, Did you check the size and flow of your fuel tank pickup, Is your fuel filter clean?
A carb will help cool the intake charge more then the fuel injection which would help.
I run a F.A.S.T. the old Speed Pro ECU on my engine works great and it's lap top programable. It has a Wide Band O2 sensor which corrects fuel mixture to helps to prevent leaning out. GEOO;)

dirty L
just my opinion but i would go with a good old carb. you don't even really need a choke down in sunny florida so drivability won't be much of an issue. reliability will be much better with no sensors or electronics to fail as well.