You state that it's an aftermarket system. If that is indeed the case, I'm not so sure any Ford dealer can help you out.
Viper alarms, among several others, are made by Directed Electronics. I can't be positive, but I believe the Excalibur alarms were made by another company. Does it actually say both of those names somewhere?
I would for sure find out the manufacturer, as well as the exact model number. You are going to need both to try and find a replacement remote. Depending on how old the system is, one may or may not actually be available.
If the way it looks is the only issue, you can probably find a case for it online. I would just do a search for alarm remote cases. Hopefully this helps a little.