Thanks Nathan. This morning I went out again to go over everything before I start to tear into anything, just to get a better visual as to what mechanical stuff is happening when the doors are shut. I noticed on the extended cab doors there is a little lever under the handle that the main door would actuate when fully shut. Is there any switches associated with this lever? I also armed the security system and waited inside the truck for just over 5 minutes, the security light illuminated the whole time, I then manually unlocked the driver door and opened it, no alarm sounded and the security light started to flash repeatedly. I have a feeling it is something to do with the passenger door or passenger extended cab door because with the key in the ignition and open the driver door I get the normal ding ding ding ding.

Thanks for the help.