AFAIK, there is only a CTM on lower level (lesser factory optioned) vehicles, maybe sports or some stripped down Rangers, instead of the GEM which when present does the CTM duty, so no (Ford of this era at least) vehicle with have both a GEM and a CTM, just CTM if the vehicle doesn't have features that need a GEM or vice versa.
I too would first look at relays, particularly the battery saver and accessory delay relays.
After swapping relays around with known good ones, if no luck then there are tests you can do to rule out the GEM. GEM just grounds the relay coils, so manually you could connect a jumper wire between the battery saver relay purple/orange wire and ground which should turn it on. Similarly you could jumper to ground a wire between the accessory delay light blue/red wire and ground to turn it on. I'd start with the battery saver relay both for swapping it and for jumpering to ground to test it because it has to work for the accssory delay relay to come on at all.
Frankly the eventual failure of the battery saver relay is common enough that I would go ahead and buy one to keep in the glovebox if it hasn't failed yet, given its age... they're about $10 on amazon. Example:
Amazon.com : Standard Motor Products RY612 Relay : Automotive
Edit: Amazon's listing is screwy, select "AC heater switch and relay" even though that's not your purpose.
Local auto parts stores may carry a different brand or of course motorcraft with a different part #. Sometimes auto parts stores want near double Amazon's price. It should be in a box up under the dash near the driver's right side footwell.
There are different relay box configurations for different vehicle years. I guess I never got around to making a comprehensive list of what each model year looks like, but this pic below "might" be the right one for a '98.
Notice how the battery saver relay is the same type used for most of the other positions. You could swap the battery saver relay with one of those as a test.
View attachment 321341