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This is possibly a fuel starvation issue. We need to run the engine on another fuel; source to eliminate the boat side fuel system as a possible cause of the issue. Disconnect the fuel line from the engine that comes from the fuel tank. Plug the line. Then get a gas can and some fuel hose connect the fuel hose to the engine and stick the other end into the gas can. Secure the gas can and hose run the boat. Does it run better or the same?
There is a test we can perform but it requires a vacuum gauge some fuel hose and a brass tee. Connect the vacuum gauge into the fuel supply line coming from the fuel tank. Run boat watching the vacuum gauge. The gauge should never exceed 2" of vacuum. If it does you have a fuel restriction in the boat side fuel system
Post back with questions and findings.
Here is a diagram of the vacuum gauge set up. The gauge can be installed anywhere on the fuel supply line.