2wd manual to 4x4 auto

[7.3-StRoKeR]

Im in the middle of this conversion i already have the trans mounted in the truck but im having problems tiring to get the electrical figured out. I changed the whole main harness up front because the one for the auto has more pins than the one for the manual. I as put in the auto pcm, but the problem is with the trans wiring harness. The truck will only start if the manual harness is in. i go to put the auto harness in and the truck wont turn over.

Do i have to jump something?

I already disabled the clutch safety switch with the correct plug from the auto. Wht else is there?

Sorry for all the questions but im out of ideas. All help will be really appreciated. Thanks