Hello,
somewhere on this site is an Explorer of this generation alarm/remote start install with some pictures in it. You'll have to do some searching for it. 2002-2005 are basically the same.
1) the 5303 has 3 trigger inputs: 1 is for the trunk, the second is for the hood, and for the 3rd its for the doors. The doors has 2 inputs to it, the green negative door trigger or the purple positive door trigger. The reason the 3rd has 2 types of inputs is to make it more flexible to the different types of cars out there. You'll only use one or the other based on what car you have. In your case you will be using the Purple Positive input.
2) The different Zones will alert your remote in different ways. When someone opens the hood while the alarm is armed you will see the hood open on your remote as it pages you. If the shock sensor goes off you will see a hammer symbol next to the windshield appear as the remote pages you...etc.
3) Yes, and you will be just using the Negative lock/unlock off the Avital to the negative lock/unlock on the Explorer. Depending on the wiring diagram you have, it may also list lock/unlock "motor" wires. Those wires you will not be using.
4) Hooking up the door lock/unlock as stated in #3 all the doors will unlock at once. You will loose that feature unless you want to add it using the 2nd unlock wire off the Avital as well as a relay and some extra wiring. If want that the doors act like the factory remote, I can list how you would wire it up.
Some thoughts:
The Positive door trigger: The easiest way to wire in the door trigger is to just use the BLACK/ blue dome light wire. This will detect all doors including the hatch and the rear glass. Therefore the trunk trigger wire off the avital will not be used. You will need a relay to convert the negative trunk trunk release wire off the Avital to a Positive signal for the Explorer to be able to pop the glass at anytime(even if the doors are locked) Now here is my thought. If the doors are locked then most likely the Avital is armed. Since you are using the BLACK/ blue dome supervision wire as a door trigger, when you pop the glass the dome light will go on telling the Avital a door is open. Will that set of the Avital alarm...hmmm not sure. I think it will. See if you were able to use the separate trunk trigger off the Avital, I know the Avital will ignore the trunk trigger when you pop the glass. I don't think it will ignore the door trigger though. SO you would most likely need to unlock the doors, then pop the glass.
Ok... Now since you would have to unlock the doors to pop the glass anyway. There is another option to pop the glass that doesn't need a relay, but requires that the doors be unlocked first to work. You get where I'm going with this? So that wire will test as a negative when you press the button on the outside of the hatch near the license plate. The best place to test for this wire is at the connector going out to the hatch at the rear roof of the car. You will see a plastic trim in the trunk on the roof at the edge of the headliner going from left to right. Pop that off and you will see the rear hatch harness. Both your Positive and negative glass release wires are in there. Test for which one you want up at that connector in the roof and write down the colors. You can find the same wires in the drivers side rear door sill. test for them there. Makes it a little bit easier so you don't have to run a wire all the way to the roof. In running wires to the roof you would have past the same wires that are in that rear door sill anyways...LOL
As for the bypass, I personally use the Idatalink TB unit as well, but that needs to be programmed using Idatlink's USB programmer. Plus to access the programming section on their website you need to be a registered dealer. I personally have used Fortin's Key-override-all or Key-override-SL2 for years on Fords and NEVER had a problem. They come pre-programmed. I mainly do newer Fords now and their encryption on the keys has changed. I can no longer use them for the newer Fords, so I use the TB now because they can be used on newer and older Fords and I only need to stock the one piece. You'll need 2 original Ford keys to program either bypass. No cloned keys will work.
Wow, ok Thats my thoughts. Other then that, its a pretty easy install. Ignition wires are easy to get to as well as the transponder wires. You won't be using the Pink/White heavy gauge wire for this car so just tape it off. Brake wire is easy to get to at the pedal. You can find parking lights at the switch or the kick panel. Door locks and Door trigger are in the drivers kick panel as well. And glass pop is under the drivers side rear sill plate. oh and its easy to get through the firewall for your siren and hood pin Switch and tach. I use a mercury switch for the hood pin. I also run a ground wire from inside out to be shared with my siren and my mercury switch. This way it doesn't corrode from being under the hood. For tach signal, use an uncommon wire at one of the fuel injectors. Avital's don't like the wire off the coil on Fords, they like the fuel injector signal.