I only know how to do it with a Gm Tech 2, I have a truck with the 8.1. When the procedure is enabled in the scan tool, the throttle is mashed wide open while out of gear, the rpm shoots up to ~4000 rpm before the ECM intervenes and the rpms drop, and then the procedure should be complete.

Do you know you have good fuel pressure when its running like crap? Could be a number of things causing intermittent fuel pressure.

Tested fuel pressure, at idle and W.O.T. all normal on the fuel pressure gage W.O.T. 44-46psi

I don't remember doing any relearn when I installed my crankshaft sensors. Just slapped them in and go.

unlike the automotive side, the Marine side does not have a crankshaft, variation, relearn,

crankshaft is not your issue, crankshaft provides input to the ECM. Let’s the ECM know the engine is cranking so it could enable injector pulse, it’s either running or it’s not, at times it could give you a stumble if there’s a spike in input ,

I haven’t read the whole thread, so if this is not been mentioned,
I would start by looking at the water pressure, if your impeller is worn or if it’s not pumping enough water it will set the alarm off over 3K, you need to look at block pressure and see what the reading is when the alarm goes off, if I remember correctly it should be about 15 to 20 pounds ,

I also gotta say, every time I read these threads an I see all the replies telling you to go buy a scan tool. I can’t help with laugh, what good as a scan tool if you have not been trained to use it and know what the readings mean, you need to go lot further diagnosing than just looking at codes, 75% of the time the code is not the actual part that failed,

it would be the same as buying a stethoscope and thinking you don’t need to go to the doctor anymore, lol

I haven't done a relearn when I've replaced cam and crank sensors in past 496HO builds. Worked fine. Maybe I got lucky.

Does the tach bounce fast from 3000rpm to 1000rpm?

It was kind of jumpy last time i put it back on the trailer, but I have not run it since then. Will be working on it sometime this week and see what i can come up with.

Not sure if this is relevant, but I had a similar issue on a 6.2 mpi. Ended up being a faulty IAC. No issues at idle and no symptoms till it was warmed up and exceeded 4k rpm. Alarm went off and couldn't get past 3k rpm till it was shut off.