I thought I had this problem licked. Race one at the Worlds last year I fried an alternator, second race developed a miss but also had fuel filter problems so I didn't concentrate on the miss. Over the Winter I notice that the nut holding the battery wire at the starter, using the large ceramic looking fuse had welded half way off against the block so I removed the fuse thinking that what may have fried my alternator. Now to the problem. Starts fine, rev to 2000rpm to energize the single wire alternator, charges fine, get on plan and with ever wave I hit I get a miss and the volt meter drops to 0 then back to 13 or so. Checked grounds, battery wire its as if you turn the key off for a split second, its not the plug either. Could their be some kind of short in the new alternator, could the module or the Thunderbolt ignition do this? Any help would be appreciated.

Sounds like the main power supply is loose. That's why your alternator looses power to it also at the same time you get a miss. If you check all ground and positive connections. If it still does it i would use a different battery to see if the battery is shorting internally.
Tom

Sorry Tom, I have been watching the tech thread I posted on the same topic. I think its the alternator. I fried the first one then maybe damaged the second one. Just ran the engine with the single wire disconnected to the alternator and seem to run fine just on battery voltage what do you think.

Eddie

Sounds like you have a temporary ground in the alternator. How did the first one fry?

I was using the merc fuse at the battery/starter wire, allowed wire to ground against block to the point that the nut was half welded off, my guess is that it fried the alternator then damaged the second, I didn't discover this until this winter