If you're sure it's running on one cylinder the problem should be fairly easy to trouble shoot. Start with getting a compression reading, both cylinders should be in the 140-150psi range. If the compression is O.K., check for spark on both cylinders.
If you don't have spark, replace the spark plug, trim the spark plug wire back about 1/4" and re-install the spark plug boot. Let us know what happens.
The reason I asked if you were sure you were only running on one cylinder is I had similar symptoms, and it turned out to be the rectifier/voltage regulator.
Lou
