I am running Dynatek Dyna DS1-2 Ignition & DS8-1 5ohm coils, stock spark plug caps & new spark plug wires. I am also using Rick's combination Rectifier-Regulator part 10-100 which is claimed to provide a little more output than the stock Rectifier & Regulator. I am also running LED lights for everything except the headlight which is a PIAA Xtreme White Plus H4 Bulb 60/55 watt and have no electrical problems after repairing the bad electrical connections.
Electrical problems can be a pain in the arse so focus on one circuit at a time
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However I have had problems with bad electrical connections, the old brass connectors being lose and even cracked causing poor performance and/or none at all. I prefer soldered connections whenever possible.
Check for loose or corroded electrical connections.
My stock coils crapped out on me causing the bike to run poorly, then only on two cylinders.
Pull a wire either 1 or 4 and then 2 or 3 attach a good spark plug to the wire, ground the plug to the engine with the engine running and see what kind of spark you have, a small weak yellow spark or a strong blue spark.