head smacking electrical issue

IDIoit

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im trying to find an issue with my 01 F250 SD.
stock engine with a 4R100

all of this came about after a stereo swap.
an aftermarket harness from the stereo harness is the only thing i cut into.


now my windows dont work until after 15-20 seconds after the ignition is turned on.

i had the computer scanned and the GEM module popped up
i went to ford and had it replaced and programed.

before the GEM replacement it would cause a no start issue when cold.
i have yet to cold start the truck, it just came back today.

issue still persists.

everything else works, overdrive, & cruise control

door locks never worked.

what can i check to solve this issue?
 

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