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Hey Jason. I had my auto PCM reburned which is essentially what you've done with your chip. With the help of several high caliber guys I was able to figure that same issue out. After the swap I ran it stock for a while and my cruise worked but when it was reburned as a manual my cruise stopped functioning correctly. I was given some good info on this subject from Jody Tipton and Jim Rose and got it working again. Here's the scoop:
I spliced Pin 29, the Tan/WH wire, into Pin 31 which is Black/Yellow. Pin 31 is the brake pressure switch and my diagram shows it to be hot always EXCEPT when the brake is applied. Anyway, took it for a test drive afterward and everything works as it should, all the cruise controls and brake disengage. I heard indirectly from Ryan Bean that you just have to verify 12v to Pins 29, 31, and 92 and as long as those check out it will work.
Rezvani's Latest Post-Apocalytic Monster Is a Ford F-150 Raptor Underneath
Slideshow: Called the Fortress, the 850-horsepower pickup combines Raptor underpinnings with military-inspired features, survival equipment, and a starting price of $285,000.