#12 and #16, one is brown, one is dk blue with white tracer if it's like my Fury. I just went through that part of the harness to correct a meltdown. I'm running a 1 wire alt and several non-stock things now, so mine is now different.

On mine, the dk blue wire goes from the key into a big splice that powers the lights as you mention, then out to the bulkhead. Definitely look at both sides of the bulkhead for those wires along with your charge wire.

You haven't added any aftermarket stuff hanging off the switch, have you?