I just had the same problem on my 2002 350 MAG MPI. Stalled just ideling, and at 4500 RPM it started running really bad, finally quit running. We had to be towed in.
No codes from the ECM. My mechanic did a lot of testing. Turns out it was the crankshaft sensor. On the bottom of the motor by the oil pan. The mechanic said it probably got wet from water in the bilge. Replaced the sensor, took the boat out and runs like a different boat.
i thought it was the ECM. That would have been expensive.
