The fact that this issue popped up after you changed some plugs strongly leads me to the possibility of it being electrical. Fuel issues tend to get the engine to sputter or run erratic prior to a lean stall. Ignition/electrical can cause the engine to simply quit. After all, that is effectively how we shut engines down via the ignition switch.

As BUP says, kill switch...look there. I'd also take a good look in and around the ignition system to look for loose or partial connections. Strong batteries are also a requirement for the ECM. It's a long shot but you might have a battery dropping a cell when at speed cause the voltage to drop precipitously. ECM says "Me no likey" and quits.

Sorry my bad I forgot you posted about the neutral safety switch already. I read it one time and just looked at it again. Yep you by passed that already.

You say test tool with no codes for scanning the engine - so which test tool - do you mean winky blinky or a real scan tool to monitor readouts ? I would use a scan tool and watch voltage output especially running and right at shut down.

Still sounds like a kill switch problem and or short of some sort. Bringing the throttle back to N to restart points me to the kill switch - asking again which control box do you have - the one in the link I posted ? Merc commander 3000 ? or which one ?

Battery voltage weak and or drops but then have to ask how does it recover in a blink of an eye to restart the engine in a split second very easily ? Make sure your batteries test good with a load on them and all connections are good plus tight with no corrosion. If your batteries are older than 4 / 5 years of age - you most likely need new anyways.

this especially over the net / fix will have to be a process of elimination fix. So the train keeps on rolling.

Asking again what ignition system and is it stock ? Have you changed any ignition components per the start of your problems ?

As mentioned before, I think a good start would be to install a known good battery for the next trial run, whether you have to pull it from the tow vehicle or not. Start simple and go down the line, you also mention new cap and rotor, but I assume that would be cough and sputter not sudden shutdown.
Coil wire?
Problem arose after tune up so I would work back from that.

I have a Test Tool. Did not pay attention to the voltage when I had it hooked up just checked for codes. Will check that first. Also will Load Test the Batteries they are old. I have the Merc Comander 3000 control. Will bypass the kill switch after I check out the voltage and batteries. Ignition is all stock. As far as I know no modifications have been done to this engine. Coil wire is new along with plug wires. Boat ran great after tune up. Motor developed a miss after fuel system plug up. Talked to local mechanic and he said as boat ran out of gas from the plugged pickup tube it leaned out and cylinders heated up. He stated spark plugs are designed to fail before burning a piston. When I pulled the plugs, found one with cracked ceramic around the electrode. Replace the plugs and boat ran great. Then it started the shut down thing. I am starting to suspect the batteries and/or electrical system. The wiring should be in good condition as I traced every wire and actually replaced some when I was trouble shooting the old ECM before purchasing the new one. If it turns out to be a battery that will be wonderful as I may have be overthinking this thing. Thanks again for all the input. Will try to test this evening.

does this system have an oil pressure swith which will shut the engine down in a low oil pressure situation but has a bypass for start up.kinda sounds likes whats happening.the starting right back up is weird part of this.I was originally thinking a fuel supply hose was getting sucked closed.
good luck w/ the troubleshooting.

More info keeps coming in of what has been done and what has been tested. It would be best to see what else the owner posts of EVERYTHING that has been done and tested to help pin point the problem alot easier. Can not stress enough about fixing boats even in your hands that the proper info is relayed and indepth totally even if it is in long story book length to help diagnose the problem alot easier without throwing darts here.

I am not saying this in a bad manner so do not take it that way. trying to make it easier on everyone. Thats it.

Old batteries and especially if the weak cost you alot more money down the road as they stress the hell out of alternator, the starter and all ignition components.

Change the batteries to new plus has the recommended proper amps - first and foremost - then proceed to see what happens. Check all connections. Are they 100 % corrosion free ??? Test and if problem stays - by pass the kill switch and see what happens. Good luck.

I already said to try portable fuel tank with fuel line and primer bulb but around third post the owner said he tested using the portable gas supply.

Ignition Module in dist.

Chris

Check the wires going to the key

Did not have time to take out and run but did test the battery. Battery tested good, it was fully charged as the boat had a charging system. Used a commercial load tester and actually really pushed the load testing, battery handled the load and still held over 12 volts. All connections are clean and tight. Hooked up the test tool and started the engine. Again no trouble codes and test tool read 14+ volts. Let engine warm up and increased the RPMs to 3,000 for a few minutes then to 3,800 to 4,000 for a while all the time watching the test tool. Ran through all diagnostics and no trouble. Pulled the throttle back hard to neutral from over 3,000 RPM a few times, The voltage stayed good. Also had the battery tester hooked to the battery during all this and it read about the same as the test tool and volt meter in the dash. Without being able to take it out and run it, could not duplicate the stall in the lift. I do not think it has a shut down oil switch, it does have a sensor on the block and a low pressure alarm, but it also has a pressure gauge and pressure stays above 40 PSI until it shuts down. I tested the ignition module in the distributor when ECM was replaced but it could still be a suspect. I do plan to check the wires to the ignition switch but they were also tested and inspected during the trouble shoot prior to ECM replacement. Engine ran fine for over 40 hours after ECM was replaced. It just started this problem last week. I still feel it is electrical like a short or a bad ground somewhere. Will try to take it out tomorrow evening and run with the test tool hooked up. Last thing I did tonight was bypass the kill switch to be ready for the test run. Thanks again for the input,

What voltage do you get on your good battery? it should be at least 12.5 volts at rest 1 hr after any type of charge and be full of electrolyte .
Also how hot does the ignition coil get? If the coil is getting hot it could be your problem.....