I'm gonna jump in here, against my better judgement, first won't rev past 4k, I doubt that it's an electrical issue, valve float that starts at 4k rpms could be lifters starved for oil pressure, rockers too tight/loose, fuel starvation, timing, valve springs. Sure I'm missing a couple things.
Installing aftermarket ignition boxes, a carburetor, different heads, programmable ECU likely will make diagnostics more difficult, sure you may stumble into fix'n it but highly doubtful.
Oh, and the 3 bar heads have a bad rap, they are really good upgrade for a stock street cruiser, just a little boost up from stock,.with the right parts,
I'd go back over my assembly procedure and recheck those things.