The dyna isn't failing while the bike is resting with a 12.9 V battery voltage, is it?
However, if the tiny battery is being charged over 15V to say, like 20V, that would stress the dyna. (Which is why I asked for a battery voltage after a long run.)
Also, in stock bikes, the large battery capacitance damps ripple voltage and noise spikes throughout the entire electrical system. A Points type ignition system wouldn't care about these noise spikes. However, transistors can get quite stressed when zapped with voltage excursions beyond their tolerance.
Does the Dyna documentation give an operating voltage never exceed value?
So, you have an ignition, battery, and charging system that is NOT stock and was never engineered to work together before your assemblage. If you want to get to the root, you may have to do some engineering, which begins with gathering data. imo
Cheers,