I posted a question a long while ago about the factory installed Ford alarm system that I didn't get an answer to. I just figured it out and thought I would post in case some was searching for the same thing...

Once you disconnect your battery you can't start your truck unless you use the kill over-ride switch. The solution to make everything work again is... Quickly hit the unlock button three times in a row, pause and then hit it three times in row again, the alarm will chirp, then unconnect your battery quickly and reconnect it. The alarm system should work as it always did now.

Hope this helps.

 

Yea, I remember your post. That was a few months back, glad you got it worked out and thanks for posting your info, incase someone else has the same problem.
Keegan