Ok so I had just about given up and actually ordered an aftermarket brake controller from Amazon. After I ordered it I decided to go through absolutely everything one last time (I prefer a factory option). Checked all the harnesses, even had the fender lining out again to inspect that.
Finally decided to go a little deeper and disconnected all of the harnesses going in the bottom of the fuse box. I was checking all the pins and noticed one didn’t look right, it had slipped back slightly. I pushed it back and it clipped in place, put everything back together and reconnected battery.
PROBLEM SOLVED!
Trailer brakes work fine now, even managed to cancel the order of the aftermarket one before it shipped.
Thanks for everyone’s input!