Running rough at low rpm

Having issues with my 2014 40 hp merc 4 stroke efi. When put in gear, lowest rpm is about 800 but finding it rough or stalling at about the 1000 mark. It can be sluggish when trolling at 1000 rpm then trying to accelerate. Anything above 1500 rpm runs fine and if i run it at those higher rpm for awhile then slow it down for a troll itll be decent for a bit at 1000 rpms.

Ive recently changed the oil, lube, inline filter and element filter. Also, ran a couple cans of sea foam and the merc engine cleaner. Only recent changes I can think of are trying to use the motomaster stablizer as opposed to the usual merc stabilizer I used and went to a new gas station to fill up before these problems started.

I avoid the huskys and mohawk pumps and will usually run the 91 or 94 and add generous stabilizers if running 89. Just burned off most of the previous gas in the tank and filled up on 94 so hoping the new fuel will resolve the issues. Cleaning the high pressure fuel pump is next.

Any recommendations are appreciated.
 
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so three key elements to motor operation.
compression
fuel
and spark.
assuming compression is good and
fuel has always had stabilizer then
this only leaves the latter.
my advice....always check for factory
gap on the spark plugs. if its supposed
to be .040 check them all before you reinstall even if they are fresh out of the package. they do vary . could have been
dropped and will effect the operation
with dramatic results.
 
Forgot to mention I replaced the plugs. Left the oem gap of .35 because I read the gap would open after some use.. Thought that would hold true as the gaps on the plugs I pulled were much wider than .4 from use but could be causing the issues at low rpm until the electrode widens to the correct gap.. Will be pulling the plugs again to do it right.
 
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Avoiding husky and Mohawk is pointless. Every gas station is now putting up to 10% ethanol in their fuel, which may be your problem.

Chevron 94, costco 91, and most marked marine fuel is ethanol free.

Change out your fuel filters, if you have any.
 
Did you seafoam etc before or after changing the plugs? You might have gummed up the plugs as a result if you did it before. Clean up and re-gap those plugs and run it hard for a few minutes next time out after it is warmed up. Bet it will run better.
 
ryanb has a good point. check both
fuel filters . there are two and drain
the water trap.....!
 
If you have a separate water separating fuel filter, change it out too. They are cheap and easy to change. With ethanol in our fuel we should expect more water to collect in the separators we run. They can "fill up" with water which will then bleed into the fuel.

Lots of great ideas here, but i would start with the plugs myself. 50 thou difference in the gap might make the difference, although you've gapped them tight, so theoretically you should get a hotter spark and that shouldn't affect low end performance. I also liked the "warranty" suggestion.
 
If it were a contaminated fuel issue it would run ****** at all rpms.
 
Both filters had been changed as per the manual (inline and the paper one in the plastic element type of bowl).

I ran the sea foam before and after changing the plugs but used it as more of a fuel treatment because the ratio to fuel was around 5:1 instead of 50/50 that they suggest as an injector cleaner.. Another thing which could be suspect are the injectors although I hope its not the injectors..

I'll have to give merc a call but Im thinking this is a result of overdue annual maintainence rather than a warrant issue.. Even though I picked it up a year ago and had the oils changed out at the 6 month mark, I put a lot of hours on it since i don't yet have a kicker for trolling.
 
Check into the idle air controller valve. Had this with my 2006 merc 115 efi....(it is the thing that makes a clicking noise when starting the motor)...sometimes they get stuck and dont allow for proper air flow after running for a while..it ajusts it postition based on engine temp/rpm ...does the problem happen only after running for a while? If so...idle air controller
 
I ran the sea foam before and after changing the plugs but used it as more of a fuel treatment because the ratio to fuel was around 5:1 instead of 50/50 that they suggest as an injector cleaner.. Another thing which could be suspect are the injectors although I hope its not the injectors..

I was having similar problems on my F60 Yamaha
I used 1/2 bottle of Seafoam in a 5 gal tank.
gave it a good 15 min run at 4500 rpm's and no more rough idle.
 
Thanks for the tip on the IAC, hadnt even thought of checking that. I just returned from vacation so no updates yet. There isn't a separate water filter but the Vapour separator tank is said to often build up water and debris which I'll look for if I have to open up the VST for the fuel pump.. I've also noticed Mercs used to be notorius for issues with faulty coils so are on the list too now..
 
Well the gaps which I read online were sup posed to be .035 were actually .028 so now it's properly gapped to .04..

I bled off the VST but havnt yet opened it up for a thpro ugh inspection. I did a coil test but all three were working fine.

I'm not certain where the adjustment screw is on the IAC but I think I see where it should be tapped to adjust it. A bit hesitant to do that though as it would make more sense to replace it if it's not working or go after the problem which is causing the rough idle. When I cover the breathing valve on the IAC, it seems to smooth out at the lower rpm but not sure the effect it'll have on the upper rpms..

Starting to think the injector are gummed up, so will likely do a proper seafoam injector cleaning.

When I pulled the new plugs to gap, I noticed the plugs where wettish with carbon caked on in patches after having run them 3-4 hours with a .028 gap instead of the .04.. Not sure what to make of that if it's running lean because of the lack of gap or combustin issues..
 
Just back from after running a gallon of chevron 94 to a bottle of sea foam. It ran smooth afterwards on a jerry can with just the fuel and stabilizer but rough again once back on the main tank. I think what happened was the sea foam is still too strong in the main tank and is bogging it down.

After the first sea foam treatment I had previously done, I refilled the tank (10-12 gallons) and added another can of sea foam to the tank as fuel treatment. May have been too much and caused the engine to occasionally bog down. Will be out again tomorrow to burn the rest of the tank off and try to avoid feeding the seals.
 
Fuel issues diagnosis was a bit early then thought it was the IAC, but turned out the thermostat was stuck open with some debris so it was running cold.
 
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