I think you over thought this one and made it more complicated than necessassary.
Installing the Thunderheart is a total rewire. If you installed it like the instructions, you no longer had higher amps going to the key switch. The Thunderheart is like the ’05 up BDM’s in that it uses low current signals to turn on internal relays to actually power stuff. Look at the diagrams, all switches go back to the Thunderheart, and power to all lights and other electrical loads come from the Thunderheart. More specifically, all wires to the key switch go back to the Thunderheart, regardless if you have a two wire or three wire key switch.
You already have the better (higher amp rated) switch, it will handle the lower current.
In my personal opinion, not really.
Heat does kill electronics, and it could be the culprit behind some dead EHC’s, but I doubt that it is being transferred from the coil area to the EHC by the wires, more likely it just comes from hot air from the engine. Heat makes wires have less resistance and then they can carry more Voltage, So if you have a load that is already trying to draw more Voltage than it can get, then you get thermal run-away; the wire heats up which allows it to pass more Volts/Amps, which heats up the wire more, which allows it to pass more Volts/Amps, see where this is going? But if you don’t have a load trying to draw more power, then what happens is that your Voltage does increase and your Amps actually decreases because of it. In the words of Sven “simple, no?”
But our Scooters just don’t use many amps to necessitate the heavy wire. He was right about low voltage wiring needing to be thicker and have thicker insulation, but only for carrying the same Watts. If the current (Amps) were the same then the wire would be practically the same size. The biggest load on our EHC should be the headlight, which is legally limited to 60 Watts (I think). Using the Watt formula of A=W/V, we get 5 Amps. Remember how small a 12 Volt,5 Amp fuse is? I think every wire on my scoot will carry 5 Amps. If we use his example of 460 Volts, for the same 60 Watts we get a little more than a quarter Amp (0.130435). So current (Amps) is the limiting factor, not power (Watts), and our scoots just don't use much (except for starting).