Caveat: I am not an expert on PATS, but since you are desperate, here is what I know. Take it with a grain of salt, please.
1) The transceiver is just a short-range radio device. It simply passes on what the key sends, so your solution of replacing the transceiver and placing the original key next to it should work. It does not matter whether the cylinder in the ignition switch came from Autozone or from a junkyard.
What I am not sure about is how the PATS will respond to your new, extra keys being around as well. Hopefully, they will just be ignored. Worse come to worse, you can break the plastic head and remove the chip from those.
Of course, as you sure know, this will allow anybody with a screwdriver to steal your truck.
2) Do you still have two original factory keys? If so, you can program the new ones as 'additional', by simply following the procedure in the drivers manual and maintain the PATS protection (which prevented the thieves from starting your truck in the first place). If you only have one key, you can still do that, and you have two options before you pledge your firstborn to the dealer:
a) Just about any better-equipped locksmiths (like at Lowes or some such) can 'clone' your existing key code onto your new keys, so you don't need to leave the key in the truck for the thieves. The drawback of this method is that to the PATS system you only have one key, and it won't let you program anything else.
b) Good locksmiths have the equipment to program the truck computer to your new keys. This is the best option, and should still be much cheaper than the dealer (in most places).
Good Luck!
Ok guys well first off, my name is Chris and this is my first post on this fantastic site. I have an issue with my 1998 Ford Explorer. Well first my Ex was attempted to have been stolen. The idiots broke the ignition along with the transceiver that reads the key chip. Now I have went ahead and bought a new ignition from Autozone. The "transceiver" one with 2 new keys with chips in them. Now my question is. If I go to the junk yard and get a new non broken transceiver, and hook it up will it work? The way I'm going to do this is to zipp tie the factory key to the transceiver so it always reads the chip. so I can use my 2 new keys I got with my new ignition. Will that work ? And another question is if I go get a new ignition and transceiver with keys from the junk yard will that also work? PLEASE HELP MY GUYS in in a rut here and need to fix it ASAP and don't have time or money at that to take it to the dealer