1 Hot Wire. 2 Breakers. 2 Circuits
After going through 20+ outlets, switches, and lights I finally found the issue. Big thank you to everyone for their words of advice. 2 black wires and "common" were incorrectly wired from a switch to a light. Basically they ran a black and white wire to the switch making the common hot (of course the white wire wasn't marked with tape) Then they tied 2 black wires together with that common at the light. I completely removed that entire rats nest of confusion and ran new wires for that portion of the circuit. My entire circuit is now GF/AF protected, free of hot neutrals, TR outlets, and most importantly only works off of 1 breaker.