Viper 791xv Transmitter Stopped Working

I am very stumped right now.  I installed a viper 791xv in a customer's 1995 Ford Windstar about a month ago.  Everything was working perfectly during that time period until today, he left his headlights on over night and his batteries died.  The customers neighbor jumped his car and the car started again.  The problem is, the transmitter doesnt work anymore for some reason.  I didnt really have too much time to check everything, but I tried unplugging the antenna for a bit and plugging it back in, taking the battery out of the remote and putting it back in, checked the thin gauge red power wire fuse (couldnt get to all of them without taking the underdash off), and I tried to reprogram the remote according to the instructions.  No matter what I do, when  you hit any button on the remote, a few seconds later it beeps as if it got no responce.  I can access menus using the valet button and the led blinks and everything, the locks also still lock and unlock with the ignition.  Any suggestions to what I should do?  This forum has been very helpful so far - I appreciate the help

nobody has an idea?

probably screwed up the antenna when the car was jump started.  It's an issue with that system.Cause I'm So white and nerdy...

First Class Certi-fried installer

ill try that jmr964..  Thanks.. I only unplugged it for about 2 minutes.