40HP runs rough

[RWestman]

I have a Mercury 40HP outboard which is currently running rough. Here is some background which might help: Last Fall someone remove the lower unit drain plug and the unit was damaged. There was a shortage of replacement units so I decided, along with the dealer, to put the pontoon into indoor storage and the dealer could replace the unit in the Spring. The motor was not Winterized, for example no fuel stabilizer. When the pontoon was put in the water recently it seemed to run okay, but started running rough. I ran all the old gas through the engine and added 1/2 a tank of 87 octane and 1/2 a tank of 91 octane fuel, along with a can of Seafoam to clean out things. Since then the engine has began to run rougher. Today I replaced the fuel filter and took the pontoon out for a run. It seemed to run GREAT for about 5 minutes and then started running rough, not as bad as before, but still rough. I have ordered a couple replacement fuel filters thinking maybe something is still causing fuel filter problems. Any other suggestions to what I should do or look at? Thank you.

 

[guyjg]

Look at the spark plugs...they can tell you how each cylinder is running. Plugs should be medium brown. Probably need to clean the carbs real good.