[schevel]

Hey guys, I am reaching out for some your knowledge. I have a Merc 5.0 Alpha 1 Turn Key Start in my 2006 SX21. Motor starts fine and runs, but will shut down completely while cruising. Starts right back up and runs another 5 minutes or so, and shuts down again.(engine diesels a small amount) I can cruise pretty good at 3000 RPM or less, and I can idle through the no wake zones. Had similar problem last year, 1 tank of gas with seafoam and 1 tank of gas with Heet and the problem went away. Already ran the Heet in the gas last week, and changed the fuel/water separator filter last night. No water found in gas. Coil is not hot to touch. Checked ignition switch wires, Kill switch, battery terminals at battery and engine block, pulled distributor cap and rotor button looked fine. (replaced 3 years ago) When motor shuts down, the gauges spike out as well. Trying to figure out if I need to chase a fuel or electrical problem. Here are some facts about the problem, any input will greatly be appreciated.

Boat is kept at private dock and sits in the water.
1st time it shut down last week was at low RPM (1200), and seemed like electrical. ( blew light bulb in my navigational light)
Has 2 batteries, and had swithched to #2 battery earlier that day.(disconnected #2 battery and problem still exist running only 1 battery.)
I hit the Kill Switch last night, and boat shut down in same kind of manor.

Next thing I was going to check for is a bad oil pressure switch, anti siphon valve, or clogged screen in fuel line.

[Hudson River Steve]

Schevel,
Is your motor carburated or fuel injected?
The fact that your gauges all pegged and you blew out a light bulb leads me to believe that you either have a poor ground somewhere or perhaps the alternator output wire is intermittent. When the alternator is spinning it must have a good connection all the way back to the battery or else the system voltage can jump from ~14V up to 80 or even 100V for a split second to seconds. Without a solid connection to battery there is no place for the energy from the alternator to go until the voltage regulator can adjust. This is called alternator load dump and can be very detrimental to electronics. You fuel injection/ignition system may be shutting itself down to save itself. Take a look at this circuit path. Just an idea. Good luck.

[schevel]

Steve, I have a carb. The previous owner had an eldebrock intake and Holly 600 4 barrel installed. Do you think the dial switch for the 2 battery set up could have anything to do with this?

[Hudson River Steve]

It's possible that the battery selector switch has corrosion or that the nuts have worked loose. Like I suggested, check the wire from the alternator all the way back to the battery. Including the main circuit breaker, battery isolator, battery selector switch etc. Make sure nothing is loose or corroded.

I would also check the main harness connector. Is it loose? If not remove it and make sure there is no corrosion. Might we worth it to disconnect it and connect the main connector a few times just to wipe all the contacts. If you lost power to the ignition wire on pin 5 (purple) the motor would certainly shut off. Check the purple wire going to the ignition coil and module.

Since you have a carburated engine and it is a 2006 I assume it has an electric fuel pump? I would check the oil pressure switch and wiring to the fuel pump. You could try jumping across the purple and purple/yellow wires from the oil pressure switch. Or you may just have a bad fuel pump.

Obviously it is difficult to diagnose remotely. Good luck.