Do be advised beginning about 2004 factory RKE became "remote control locks & alarm" according to my EVTM for that year. Its features are controlled by the Vehicle Security Module (VSM) which is part of the CAN-BUS network.
(FWIW my '03 has the clunky module installed near the B-Pillar base, left side--its an actual visible device you can't miss assuming that area isn't covered with factory paneling or other built-out covering of some sort.
Given that fact it could be 100% possible to obtain Ford remotes, have them programmed to work as they should. There might be a "hack" to DIY program them but I don't know if that's possible or is a dealer-only sort of service.
Checking YouTube for something related to the E-Series might give an idea how to do this DIY.