Okay I'm starting to get confused again.
So as long as I keep the junction box the Yellow/Red wire connects all the grounded safety switch wires, and proceeds to the starter solenoid where it receives +12V. So
Ground ->
Safety switches ->
Junction Box ->
Yellow/
Red ->
Rectifier ->
12v
I'm not really expecting to ride this in the rain for racing, but after I mock the harness under the seat pan I've made I plan on 3D printing an enclosure for the whole mess. Well, except for the Regulator/Rectifier as I think that needs some airflow.