I have a 2005 GT which had similar problems here was the fix for the leaking, also had electrical problems which followed, i hope this may help.
perhaps this will help out others who may encounter similar problems. My Mustang is not my primary transportation, so at times it may sit up for six months at a time. Here in New Orleans, there are many trees and leaves fall year round. The Falling leaves had gotten into my cowl drain and plugged it up as they began to decompose. when the cowl drain filled in water, water began to flow into the passenger side of the car from the area of the glove box. Eventually the floor pan filled up with water enough it came into contact with the electrical system (fuse block - generic electronic module). The fun begins... Just about anything and everything began to go haywire. From the Airconditioner to the windows there was some kind of malfunction, which just did not make any sense.
To get the cowl drain working properly, you look abuot halfway down the firewall on the passenger side, there will be what appears to be a triangular (funnel shaped) rubber boot. you may clean the debris form the bottom, reaming it out with your finger or pull the whole boot off and clean it then. If you choose to remove the boot, i would recomment enlarging the drain hole to facilitate quicker draining and less of a chance for debris to get stuck.
I began with removing the kick panel and cleaning the terminals which were exposed and the individual fuses, a glimmer of hope began but was soom quashed, when the problems started up 15 minutes later..... Did it again, same results, ouch.
Time to get nasty, unbolted the fuse block panel (GEM module), and to my dismay, there were six more plugs on the unexposed side. I tried spraying them with contact cleaner and reassembling everything. That fix lasted about 10 hours before everything went nuts again..... Getting Frustrated.
Now, it's time to get really nasty, hey what did I have to loose living in the city, i cannot drive around a car with intermittant headlights, with windows which won't go up when i park it. I pulled the GEM module again this time i pulled off the covers, broke out my trusty Dremel tool with a stainless steel wire wheel and went to town. Carefully, i polished every terminal connection (to ensure they did not bend and get misaligned), pulled each fuse (in order to access the opposite side of the circuit board) and polished all those terminals including the fuse block terminals. while disassembled, a close examination of the printed circuit board was conducted. some of the soldered connections had begun to corrode. Some of the corrosion had bridged the "channels" of the circuit board. I CAREFULLY cleaned the corrosion using a small dental type pick and a pencil eraser to remove the corosion. CAREFULLY I reassembled the covers (to avoid bending the terminal pins) and reinstalled it into my car.
Three days and counting, I have not reinstalled the kick panel (give it a week) but all seems to be going well..