Well depending on the system. With the systems I generally use (DEI) the door trigger INPUT wire can be connected to the domelight supervision wire of the vehicle, then be programmed to ignore the delay. See, what normally will happen on a vehicle like yours is when you close the door the domelight stays on for a length of time. Now if you connect the door trigger input wire of the system to the domelight of the vehicle what happens is the system thinks the door is still open. On the DEI sytems this gives a confimation chirp which doesn't effect the system per say...it still fully arms once the light goes out. But by programming it to ignore the delay all that really happens is a normal arm chirp and the system waits about a minute before it recognizes the door trigger. By that time the light is out and it normally arms and protects the entry points.It does not change anything about the way the vehicle works...this is done as a time saver since on the fords like yours the GEM module needs to be double diode isolated to avoid false alarms and those wires are a little difficult to access...but can be done if you choose so. I normally use the domelight wire and program to ignore the delay..just makes sense to me. But if you choose to go to the GEM module you do not worry about the domelight delay since these wires are before the delay circuit..basically right from the door switchs, just more of a pain to do it that way on most newer fords IMO.
As far as the domelight supervision OUTPUT wire of your system what that does is turn on the interior light upon disarming of the system,,,to me a waste since the light comes on when you open the door automatically.However some vehicles also turn the light on automatically upon unlock anyhow so this feature may work automatically with no additional wiring. I believe this feature is added as an option for "safety" but IMO if someone was hiding in the vehicle it would be strange that they broke in just to wait for the owner and the light coming on would do any good..well I thinks it's silly. If your that paraniod just keep an attack dog in the vehicle all night and carry a large polo mallet around.
"I was told by the guy i bought the system from that the factory settings like having the headlights/parklights/domelights stay on after turning the truck off can be made to still work like factory but would require using some relays."
This is where I think there is confusion. If your truck is designed from the factory to leave the lights on after the truck is off I don't see why this still won't happen by installing an aftermarket security. You will be tapping into certain wires in your vehicle but you won't be changing any of the normal factory functions..if anything you will be adding functions if you so choose, but I see no way that you should lose any existing functions. What may happen is the lights will turn off automatically once you arm the system since the doors will lock. If thats the case and you are concerned simply wait before you arm the system..the range of the remote should allow for this..or program the system to "passively" arm and lock..this way it waits for a length of time and arms/locks automatically..you will not need to press the remote until you disarm. I see no need for relays in this case.
I don't like tilt switches unless it is a sophisticated electronic type because a simple tilt or mercury switch has no way of knowing if the vehicle is on a hill so it either can false or not work when needed..it is a lazy and cheap way to protect anything IMO. Use a quality pinswitch and put a dab of grease on it every few months..if installed properly(away from water) I have found years of reliable service can be expected..some vehicles have a factory hoodpin as well and you can tie in to that in most cases. BTW I recently read that the US gov. is limiting the use of mercury so mercury tilts will be obsolte eventually.
Yes, you will strip back the insulation and solder your connections for reliability. If your connection goes bad it should not effect the vehicle because you are not cutting the wire...just tapping into it for the signal. However, the starter kill will require cutting the factory crank wire so be extra careful with that one or you might get stuck one day. What I do is after I solder my connections I insulate with quality electrical tape (3m super 33) and then put a zip tie around it so the tape will never come off and the connection has more integrity. And yes to the key..when using bypass modules that require part if the key you can cut the metal or what I do is take it to a grinder...not so much for insurance purposes per say but in the rare event a thief was to find the module at least they would not be able to start the vehicle with the key itself.
Hope I helped