Ok, after a lot of trial and error, I discovered that I was not supposed to cut the red wire. I just hooked up the blue and green wire from the PAC up to the red wire from the HU. The red wire from the PAC to the yellow of the HU and then the black wire from the PAC to ground. It worked then.
Of course, I did this after programing.
I also had to run a constant 12v from the battery to the yellow wire of the head unit.
BTW, I have a 2003 Ford SVT Lightning(F150).