Have a 97 EVO (only 6000 miles on new motor from Harley) have Screaming Eagle heads, pistons, SE57 cam, Mikni carb, Crane Single fire ignition, adjustable pushrods and Daytona coil. Bike ran great untill recently. Several times now, while riding between 60 & 70 mph the rear cylinder quits. It starts to fire again after a 5-7 miles. Thought at first it was plugs or wires but I have changed both (twice). Coil is new (only had it about 6 months). After last event I replaced the intake manifold gaskets. Anyone have any ideas I can try before takeing to HD dealership? Hate to take the bike there and the problem is intermittent.

Update: did some online research on my ignition module and found there was problems reported with the exact same symptoms as my bike. Changed out the module and 60 minutes later the problem was gone.

 

I see your ignition is a single fire, is your coil a single fire also?