Check for water in the gas. Completely flush the fuel system, there is also a water/fuel seperator on the actual engine that can be replaced, you can bleed the lines by pushing on the small tire pressure looking fittings, and replace your gas with fresh gas if you can - otherwise put some dry gas into the system. Also, Mercury makes a product called 'Quickleen' that will help clear out a lot of the gunk in there - add an ounce to 6 gallons of gas. If you don't have one, add a fuel/water seperator next to the outboard mount - you'll be surprised how much water is in fuel when you can see it and that will allow you to drain it periodically.
The newer engines are extremely tempermental with gas because their consumption is so much lower than the old 2 strokes which would discharge any of the fuel/water/oil they didn't burn. If any water gets into the fuel system they want to shut down. Very frustrating! I use Mercury engines commercialy, and have 2 50hp 4 strokes and a 75hp optimax that had water issues this past summer from rain that got into the tanks. All three engines needed to have the fuel & water flushed out, filters changed, etc. and then they were good as new. Find a good Mercury dealer who knows their stuff and can take care of you, but I have a hunch that might be your problem.