The wires will always be warm, one fix is to find a way to get more air to your regulator. Honda uses rare earth magnets in their stators, so, they produce some really good voltage, unfortunately, they don't put big enough heat sinks on their regulators. (mho) I've got a 929, and had the same issues, its common among honda's, and to a lesser degree other makers as well. try to get more air to the regulator, keeping that cool will help the whole system. It is the weak point.
The backfire is weird, but, evidently, not injurious, you'd have know right away if it had been..I would think.
This is where Wes will chastise me for thinking its the regulator again

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2000 CBR929RR- Cams, Micron cf pipe and headers, Power commander 3 (custom mapped), heads, decked, ported, polished, zero gravity shield, Frame sliders, polished frame and swingarm, remote controlled red neons, Stainless Braided front and rear brake lines. RK 520 race chain and -1/0 Vortex sprockets, bitch pegs and rear seat removed, OEM rear seat cowl, Pirelli Diablo Rubber.