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I had a similar problem that took me months to track down because I kept tellingmyself it was carb/fuel. Turned out it was the MSD coil. Would run fine for awhile, then run rough or die. Replaced the MSD box - no change; replaced the MSD coil - problem solved. I was using their heavy duty vibration resistant coil, but it still failed. Also, be sure you mount coil vertical and away from heat; mine was bolted to the front of the head on my FE; I put a 1/2 inch insulator between it and the head after I replaced the coil and confirmed that the problem was fixed. It's been about 10 months now without an issue.
Hal
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