I believe Jeff may be on the right track regarding the lower crank seal.
If I'm remembering correctly it's almost identical to the upper seal (Merc calls it an oil seal).
It's a thin metal (cup - kinda looks like the little cup on a tea light candle with a hole in the middle) the hole has a little rubber (sleeve) around it with a round coiled spring integral to the rubber (which is integral to the metal cup).
Over time, from the rotation of the crankshaft, the rubber gets worn out and tears leaving a big gap (the spring starts rotating as well around the shaft = no seal.
Now the motor can run apparently well even with a torn seal (my 15 horse had a torn upper for 3 years before I got around to finally replacing it - my motors always end up at the end of the work list

).
One of the "signs/symptoms" of a busted seal is having to richen the idle screw or fiddling with the timing (neither of which should need adjustment after initial set-up).
If the seal leak gets bad enough, such that it's now sucking enough air that it drastically changes the air/fuel ratio, you need to add more fuel (many more turns on the idle needle than normal) to compensate for the extra air in the crankcase.
However, if it's only the lower (or upper) seal as the case may be, you end up with a "balanced" cylinder and a very rich running cylinder (one plug significantly darker than the other) - plus you are burning more fuel and loading up one cylinder with more carbon - all bad scenario's.
The seals can easily be "picked" out and replaced with simple tools (I use a socket just a hair smaller than the race that catches the edge of the seal and tap them back in with a hard mallet).
The seals themself run about 13 bucks each - it's a quick job and since you just replaced the base gasket (so know how to pull the powerhead as well), it shouldn't get torn up if you pull the powerhead to get at the lower seal (normally you would replace the base gasket along with the seal).
So for the minimal cost and an hour of your time, I would be inclined to replace the lower seal since it is indicative of your current issue (and would also have accounted for the cough).
At worst, you would never have to do it again for the life of the motor (or at least 20 years)...