What's your voltage at the battery at idle?
A bad alternator, charge wiring, or voltage regulator can cause excessive voltage which can then smoke certain circuits.
If you get 15+ volts at the battery, then I'd be checking the charge circuit first, then the voltage to the alternator field to rule out the alternator or regulator.
It's uncommon to have coincidental failure but it does happy. But usually it's something related to recent changes and depending on where you tapped into certain wires, it's possible the regulator isn't functioning right.
