360 Magnum with stock EFI engine codes

You need to have the 99 ecu flashed to manual trans programming to get rid of the RE trans codes since you are running and RH. The battery temp sensor color codes for the wires I can get for you tomorrow. Why, why, why, are you not running front o2 sensors? They are necessary.
I'm no expert but that engine will barely run without an 02 sensor.