Almost sounds like a flooding issue, which will happen if there's no spark for a second or so. Although all the suggestions are good and should be checked, if I had to put my money on any one of them I'd probably go with what THEFERMANATOR said. To me it sounds like a hi-low problem with the stator. Don't forget your engine is turning at several thousand rpms. At just 1000 rpm loss of spark for even one second means that your engine has revolved 16+ times without an explosion in the cylinders. More than enough time to flood and or start to foul the plugs. IMHO. 
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1987 V20 w/1987 150HP Yamaha on a Shoreland'r Trailer
1978 16.5 Airslot w/1996 120HP Force on a Four Winns trailer
1996 V21 w/1993 200HP Mercury on a Shoreline Trailer
All towed by a 5.7L Hemi Durango.
If God didn't have a purpose for us we wouldn't be here, so
Live simply, Love generously, Care deeply, Speak kindly.
(Leave the rest to God) 
Silence, in the face of evil, is itself evil. Not to speak is to speak, not to act is to act. God will not hold us guiltless.
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