Do you have a sunroof? check the drainage tube.

Is the screen bonding secure with no compromised sealing. Water can
run along channels and wiring for some distance before it finally
comes to rest in the foot well. That means that it is conceivable for
water to manifest itself in the back foot well when the ingress is via
the windscreen! Tiz a sod to locate!!!! (As you have found!!!)

Replacing the weather seals on the door fixed our flood problems...

Did you have the air cabin filter serviced?  There have been many
reports of this causing leaks.

Search google Groups  for "Focus wet foot well" and "Focus pollen filter"
and you will have lots of reading.
Here is an instruction about fitting the pollen filter that may help to
locate the appropriate parts:
http://www.myfordfocus.com/how-to/cabinfilter.htm
/per

A very common problem due to an improperly sealed access panel to
the cabin air filter.  Every Ford dealer should be aware of this problem.
The access panel is in front of the windsheild on the passenger side.

--
Don

Facts are stubborn things, but statistics are much more pliable.
~ Mark Twain

Another possibility:  if leaves have plugged the air conditioner drain,
condensate water backs up and drips from under the dash, wetting the rug on
the passenger side.

I will bet that it is coming from the cabin air filter place.  I have never
had or messed with the cabin air filter and a couple months ago discovered
water on the passenger floor board.  I live in the desert so is not a
problem except for the past couple months with all the rain we have been
having and now I am starting to get a mildew smell.

It's a common problem. There is a TSB from Ford with the fix. Rain water
comes in via the pollen filter and or the windscreen seal. Your dealer
should be aware of this.