Is it leaking at the windshield or the cowl area? Was the windshield
seal replaced recently? Is it dried and cracked? My 66 was leaking
from right above the rearview mirror when it rained. I had the
windshield (and rear glass - fastback) pulled and new seals installed,
and that solved the problem. If the windshield was recently replaced,
it could be that the seal is not installed right, or there was too
much flexing before the adhesive had time to set properly. In which
case I would take it back to the glass outfit.

If you mean when water enters through the cowl opening and drains into
the cabin from under the dash, then you have a problem. There are
drain holes at each side of the cowl area (hidden by the fenders)
meant to drain water that enters the cowl area while allowing air into
the cabin. If those become plugged with leaves, etc, it can lead to
rust which can eat through and allow the water to drain into the cabin
from under the dash on each side. This in turn can lead to the floor
pans rusting through (eventually). This was a common problem with
early Mustangs. An alternative to rusting through under the dash would
be the drains are clogged and the water backs up until it reaches a
point higher than the vent pipes (looks a bit like a stovepipe hat -
Abe Lincoln style), then overflows into the cabin. If there is no
damage, simply clearing the drain holes and keeping debris out of the
cowl should take care of it. (the use of a cowl cover, about $30, or a
car cover to keep leaves and such from entering through the cowl vent
would be a good idea.)

Step one is get those drains cleared of any debris. Step to is to
examine the area for damage (ie rusted through).

Then comes the option, depending on how bad it is, of using a repair
kit, which consists of a pipe the fits in there and is sealed and held
in place (not sure if it was by screws, rivets, or adhesive) . If it's
too bad, you need to go the next step. available through many Mustang
parts vendors.

Worst case is you have a major job ahead of you which required
drilling out the cowl area welds, removing the cowl section, repairing
the damage, welding everything back in place, and refinishing. One of
the more expensive repairs listed for a 65/66 car.

If you go to www.mustangmonthly.com, or www.mustangandfords.com and go
through their Tech articles, I know some time back one of them did a
pictorial of the major repair method.

The following diagram is a simplified idea

________________ _ _ _ ___________________cowl vent level

~~    __  ~~~~~~~H2O~~~~~~~~~ __~~ not draining
0___|    |_________________________|   |___0-->normal drain
                                                                 |
   Abe's hats                                             \/
                                                               cabin

Hey! Spikey Likes IT!
1965 Ford Mustang fastback 2+2 A Code 289 C4 Trac-Lok
Vintage Burgundy w/Black Standard Interior
Vintage 40 Wheels 16X8"
w/BF Goodrich Comp T/A Radial 225/50ZR16

I've read the web sites on replacing leaky cowl parts, but I am not sure I
understand why you wouldn't just seal the cowl up solid.  What purpose is
there in allowing water to run in there?

Thomas