I've got a C5 ignition also on a CB 650 CafeRacer.
I also have/had issues. On my bike it was one of the coils that caused problems. Always the same coil!
I must admit, I ran them on a switched 12V sources, contrary to what the manual says.
This one coil got heated so much even smoke came out of it.
After cooling of a bit (between 15 to 20 minutes) I could ride again.
A couple of weeks ago I did not stop the bike when the issue arose. I kept going on two cilinders.
I did this for about 5 to 6 kilometers. By the time I arrived at my destination, there was so much smoke coming from the coil that my relatives thaught the bike was on fire.
The coil was completely toasted. I had the older type coils (the wiring coming out of it). Right now I have the newer type with screw terminals.
The C5 ignition is sensitve to voltage spikes the old reg/rec from these bikes.
Right now I installed a dc-dc voltage stabilizer as powersource for the coils. They get 12V, nothing more than that.
My bike:
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One of the coils:
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These type of coils are the correct ones for 4 cilinder engines like ours. Check the PowerArc site for more info. The C5 ignitions are PowerArc ignitions. I'm very pleased still with the C5 and Paul.
Kind regards from far away (the Netherlands).
Herbert (jueby)