BBQ, do you know what system they installed? If you didn't get Ford remotes, they may have installed a non-Ford aftermarket system. If you had a separate starter remote, they may have installed the starter-only system.
The systems we're talking about on eBay have full-feature alarms built into them as well as remote start and were the OEM Ford "Dealer installed option" at the time-- when you install them over an existing factory system, they will control turning that system on and off. The systems that I bought for $50 on eBay each came with two Ford remotes.
My Explorer had an old Viper alarm system on it which I removed completely before installing the new system. The Ford system adds all the extras like illuminated entry and exit, door locking with ignition and unlocking with shut down, automatic arming, valet, flashing parking lights, siren, etc. Most of these features can be turned on or off with programming. Some of them which involve connecting a wire, or just programming are listed in the instructions as installation "Options" indicating that a dealer might charge extra to hook them up.
When I was looking into this, I read somewhere that Ford was switching over to plug-in modules for the new vehicles that are more integrated with the factory wiring/computer controls. I think that's why a lot of dealers are unloading these older systems which are just Ford-branded Code Alarm systems. It's a great opportunity for people with older vehicles to get a good quality set up and add some cool features to the car. I really like the illuminated entry/exit on my old 94.
Edit: Sorry about your truck by the way. Such a shame to see such a beautiful X go. I hope to see you building up a new one soon.