I drove through some water and now my 1993 300D factory Alarm goes off contuniously and the power windows went down down I disconnected the battery. I found the module under the floor on the passinger side and the module under the back seat on the driver side what can I do?

Your problem is your BCM or known as body control module is looping into theft mode and in return not getting power to the starter so I'd check with ford on a BCM flash to factory default settings hope this helps you

Aftermarket alarm system?? If so it could be anything with that alarm. If it's the factory security system, this is totally normal. When you disconnect the battery and reconnect it, the system resets and automatically "panics" because it saw the power failure. If it's the factory system, simply have the key fob handy to turn it off after you connect the battery. If you don't have a remote fob, just put the key in the driver's door and unlock it. This will override and shut off the system.

You have not disconnected it, even if you think you have, the car would not start. It is not that easy my friend.

Battery Disconnect or Replacement Problems

Under the dash on driver side the alarm box is usually placed there. You should be able to unplug it from power there.

its lost its memory ,hold key in lock and close window then holding key in closed position for 10 secs should reset the memory in the electronic control box on the window motor memory inside this control box

Did you check the alternator? if it is faulty the car will drain all the power from the battery until it goes flat

If it's after market, just disconnect the power source. If it's factory, good luck! You might verify when you lock with the key, you unlock with the key. Don't reach through the window and unlock. (if window is down!)
A lot of cars are integrating the alarm and everything else through the radio. Have you changed or upgraded your radio lately? If so , you will need to get new code for the radio to match the car system.
Really hard to guess on an alarm system. Sorry!

sounds like the factory alarm is keeping it from starting.

Do u have the key fob to turn off the alarm, or is it not a factory installed one? Just disconnect the negative battery cable and charge the battery, that will disable the alarm while u charge the battery.