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Do you have a multimeter and know how to take basic voltage measurements?
Ok, different boat manufactures use different color wires, but on the back of the switch there should be a red, and a purple, a yellow and a black. With the key off, see if there is power to the purple or yellow wires. you are looking for around 12V. Use the black as the ground
With the key off, there should not be any on them. That is why the engine will not turn off. You have a bad key switch.
Unplug the connector between the engine and the boat. See if the pump still runs or not. You could have a stuck relay on the engine.
The key switch would be the most common issue, that is why we start there.
do you have the serial number of the engine handy?
The engine serial number wil be on the flame arestor on top of the engine. It will atart with a number, then a letter, followed by 6 more numbers.
The first one was it, I just needed to separate it.
On top of the engine you will see a solenoid with 2 large wires and 2 small wires. test both the large posts with the key off and make sure that only one has power to it. If that is good, unplug the ECU and see if the fuel pump will stop.
That is the brain on the engine. It should be mounted to the right side exhaust manifold.
You have a short in the main engine wiring harness. You have already eliminated the key switch and boat harness when you unplugged the engine. Unplugging the ECU eliminated it. The only thing left is the harness has to be shorted someplace. Look for a worn or burnt spot on the engine harness.