Ait2 Help. reads -40

[SlowMo]

2013 track pack GT. i put a gt500 supercharger on it and wired up an AIT2. splice pin 36 and put a pin in 56 if i remember right. and everything works fine. i do an automatic swap in it and put a 6R80 in it. get a new tune from lund and the ait2 is turned on but it reads -40. i test the sensor and its ohms out ok so i load an old tune from when i had the mt82 that i know it was turned on in and still reads -40. i unplug the engine harness from the pcm and plug it into the manual pcm and now the ngauge shows and reading for the iat2 instead of -40. what am i missing? do i need to move the pin for the auto pcm to work?