Okay, its the ECU.
I just swapped my buddies unmolested ecu from the same year busa and turned it on and let it run. Wouldn't you know it, the fans came right on at as they should once temps got up there.
Guess I'm calling my tuner tomorrow and talking to him about it. Thank you everyone that gave me help and advice. I suspected the ecu was to blame when I started this post, good to finally know what the problem was.