I have the same problem.
First my dealer said that they were "aware" of a leak that occurs on the Focus on the passenger's side. They said that they were going to install a "cover" over the intake opening. I asked if this was a 'Ford part' and the dealer said: YES.
The dealers "fix" was to remove the passenger's cowl, remove the drain lip that is attached to the underside of the cowl and then take a piece of sheetmetal and basically 'cover' the fresh air intake opening. This was the "Ford part" that they used.
In the process they damaged all three cowling pieces - the driver's, passengers, and the lower which is the piece that both the driver's & passengers snaps into and the brake fluid reservoir, for example, is attached to.
Each of the four times that I experienced water on the passenger's side the a/c had been used on all four of those days, but on those four days, respectively, it had been raining or rained later in the day, was cool and relatively damp out. I assumed that it was an external water leak.
In one case, there was water running from under the dash and the blower motor, which indicated a leak from the cowl opening. This is possible because I had installed the cabin filter, used butyl caulking (which is what Ford recommends using, in the repair manual and it is like an asphalt or tar type caulking) that did not seal the cowl to the windshield properly.
The other three times I had the new cowling parts (that I installed, and not the dealer) and there was no leak from under the dash as described previously. Instead the water came in from around the drain through the firewall.
Another thing to be aware of is that under the rug there is the following and starting with the rug:
Rug
Felt insulation/padding
Neoprene padding where the floor meets the firewall
Styrofoam insert under the neoprene padding
The neoprene padding will take forever to dry out and be very careful when pulling the rug back after having removed the interior panels along the rug edge. The rug is attached and held in place to the car under the interior panel via a plastic 'clip' that is glued to the rug. If this 'clip' is removed from the rug there is no way to effectively reattach it and you risk having the rug pop out from under the interior panels when everything has been put back in place.
I don't know what else to suggest, because I have yet to take the car back to the dealer and deal with them.
The passenger's cowl is about $50.00 and comes complete with clips. If you buy the clips separate with the little white pins, you can only use the little white pins because the clip assembly is welded to the underside of the cowl. So unless you have a plastic welder and can save as much of the plastic from the cowl that is melted over the clip to keep it in place, replace the cowl. It will be quicker and easier to do so and while you're in there, replace the cabin filter.
Hope this helps.