Electra Glide electrical problem

[electrahog]

Scooter is a '92 Electra Glide Ultra. Screaming Eagle accesories, Mild Cam and rockers. Power Arc electronic igntion system.
Now I believe I'm mechanicaly inclined and have been keeping my rides on the road and out of the shops for 35 years. But this one got me pulling my hair out.
Our scooter broke down a month ago as we headed back home after a 200 miles club run. Plenty of fuel in tank and suddenly the bike shuts down as if out of gas.
No spark from either plug when checked but after sitting for 10 minutes the bike started. A few miles later, same story... Finally battery was too low to turn the EVO over.
I also noticed that the alternator wasn't charging.
What I've found to date; Instead of the regulator going directly into main breaker, it was going through a 40 amp blade fuse. The fuse had melted shutting down the charging system. Traced it to a faulty regulator and re-wired a NEW regulator to factory specks directly into 30amp circut breaker thats bolted onto side of battery box.
Seems ok and the breaker hasn't popped. But after 20 minutes or sooner, engine shuts down as if key turned off. Sometimes starts and stumbles, other times will just crank and crank. No spark when this happens.
Power Arc or P/A seems to think its there electronic igntion. I had diagnosed coils but as P/A said; both coils hardly ever go bad.
Has anyone come across this problem with electronic igntions? My main problem is, I am a transplanted Yank living in New Zealand with Kiwi wife. Parts are VERY expensive here...