2005 40 HP Merc EFI stalls after 20-30 minutes

[bearcat521]

I have a pontoon boat I bought new in 2005 that came with a 2005 40 HP 4 stroke EFI Mercury engine. The engine has never given us any trouble in all that time, and always started right up each season. That holds true for this year, but a few weeks ago we pulled the boat out for a long hot weekend to replace the deck boards and flooring. We removed everything from the deck to do that, but didn’t touch the motor itself. After finishing the new floor, putting everything back on the boat, and putting it back in the water, we now have an issue with the engine that the RPMs drop and the engine sputters and stalls after 20 to 30 minutes of continuous running. It runs great up to that point, but then it stalls and runs rough. If we shut off the engine, and then restart it, it runs fine for several minutes before running rough again. If we let it sit for a longer time, it will run fine for a longer time before stalling again.

I’ve replaced the impeller (the old one had a broken “fin”), the primary fuel filter (the old one was very dirty with gunk in it), the fuel lines from tank to the motor, the thermostat, and am going to put in new plugs though I don’t think that’s the issue. I keep thinking it had something to do with stuff we took off rather than the motor itself, because it ran fine before taking everything off. Because we had to remove the tank and tank hoses, it seems it might relate to that, though the tank was empty when we took it off, and after reconnecting everything, we filled it up with non-ethanol gas before putting it back in the water.

Any ideas on what else it might be? I’ve read coils could be a problem that occurs after the engine is hot, but that’s a pretty expensive part to replace if its not that. Could it be the secondary fuel filter? Maybe the tank isn’t venting? Maybe there’s still gunk in the fuel lines? Maybe something wrong with the gas tank itself? I can’t help but think its something related to us removing the tank and fuel lines instead of something in the engine itself. Any suggestions would be appreciated.

 

[coasty14]

I would check all of your fuel line connections from the gas tank to the engine. You may have a very small leak where the engine is sucking air into the fuel system. If you have a way to test spark on each cylinder I would do that. If you have spark, chances are your coils are fine. While you were replacing the deck, did you plug the main fuel line to ensure nothing got in to it? Lots of plywood cutting and dust in one of those jobs, could be that you have a blockage of fuel flow. Also, check the vent hose on your tank to make sure it is not crimped at all. the engine will run fine for a bit, until the fuel system has no air venting into it. I find that any prior work recently done to a boat is usually the culprit for a new problem.

 

[bearcat521]

Thank you very much for the reply. I did not plug the fuel line, and yes, there was sawdust and old carpet fibers floating around. I did check the vent hose and its not crimped. I think your suspicion of clogged fuel lines might be correct, due to me not taking appropriate care of the fuel system while it was disconnected. I'll check the spark at each cylinder and the fuel lines as you suggested. The 15 gallon gas tank is plastic and over 15 years old, so I may go ahead and replace that as well. I've seen the fuel pickup tube can start flaking over time and that might be part of the problem as well. Thanks again for the reply.