Here is my post on the subject. I have a copy and paste copy of it so if it repeats what ohters have said thats why.
I had a nightmare with my water leak. Hope this helps
Check under the hood along the fire wall. You will see two black rubber drains spaced a couple feet apart. Put your finger in them to see if they are clogged. If they are clogged unclog them.
If that is not it next check the grommets on the passenger and driver side. They lead into the fenderwell that would be ahead of and above where you feet go. The others are where the wires enter the car in the door jamb area. Make sure both grommets are in place.
If these do not fix your problem continue.
If you take off your cowls you will see 10 grommets/mounts. You can either buy the new updated ones that need a heat gun to install or you can buy T2 Ford sealant and seal over them. Also you will see a pinch weld running the length of the cowl area. You can fill in the pinch weld with the sealer.
Last but not least is what was wrong with my car. Under the fenders near where the door, cowl and a pillar meet there is a seam that runs from the apillar to the bottom of the car. Mine was falling apart and was letting water into the car. It is a very time consuming fix as the fenders must come off. But I had this fixed and so far my car has not leaked since.
http://www.allfordmustangs.com/forum...sb-list-5.html
The above post is the TSB for water leaks.
I hope just your drains are clogged as that is a real easy fix. If your drains are fixed you can cut off about an inch of them which will make it easier fro large debris to flow through and not get stuck. If you pull off your cowls it would be a good time to change your cabin air filter.