Can anyone help with a troubleshoot process for the following:

Engine stalled when coming up on plane. Engine starts and on idle will die out and stall. Fuel pump or regulator are making are making noise like they are straining or starving for fuel. No alarm sounded. Scanned ECM with scan tool showed no codes set. Replaced water straining filter, water and deposits showed up when filter contents were poured into a clear jar. Boat is a twin. Gas is fresh and treated . Other engine runs normal. Thanks for any help on decision tree for diagnosis.

I would start with connecting a fuel presure gauge to the fuel rail , the valve is next to the header tank .

I will try that today. 42 psi key on engine off right? and then when idling. What would be the go/no go here? If 42 psi key off?

This is a good thread with same system:

http://www.offshoreonly.com/forums/g...oading-up.html

Yes, start with fuel pressure and work your way back to the tank.

Was this gas recently treated and hadn't been before?

There is a small screen on the inlet of the boost pump (not the high pressure pump, but the one by the fuel filter). This screen is upstream of the pump and filter and therefore is the first thing to catch any garbage coming from the tank. The filter does a good job removing water and fine particles, but anything bigger gets caught in this screen which quickly clogs up. My bet is that this is your problem. Clean it out and you're good to go. Easy depending on access to it.

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There should be a filter before this pump.

Thank you all for the direction. PSI Result: Pressure key on motor off 42psi. Drops to 38 psi. Key on Motor idling 38 PSI. I will try the Boost pump screen cleaning and fuel line vacuum pressure test (< 2 psi?) and report back.

Also yes in line filter before water separating filter before boost pump (Gen. II Cool Fuel).

Gas had been treated and is treated but may have introduced water from running without fuel cap for a short period?

Yes and no. My '04 came with the in-line metal canister filter between the tank and the boost pump but then Merc was telling people to remove that filter if there were issues with fuel pressure. Mine was removed by dealership the first year due to problems with fuel pressure. Been running without that filter for 12 seasons with no issues since.