Well, if it gets really clogged it'll stop draining and the evaporator core will end up taking a crap on you. I don't have a service manual CD for your year, but on most vehicles, on the passenger side near where the carpet meets up with the firewall, if you peel that down, you'll see part of the HVAC housing leading to the firewall.. which is usually lower than the rest (this is the drain.) On some vehicles, you can simply drill a 1/4" hole in to the drain tube, then use a coat hangar to push debris out, then plug the hole you drilled with RTV or a plug.
Sorry I don't know the exact location.. try a google search for mustang drain tube and you may find more info.