Leaks are hard to trace- best of luck to you .
I'd start with the window on that side myself if there were not obvious tears in the hatch or door weatherstrip. There is a special type of sealant that's used for auto windows which you can only get from a specialized store. Most general auto parts stores will not have it. I'd contact Mike in the Hilbish Ford Forum to get the stuff that Ford uses. It will cost about $20 a tube. When I did the windows on my Aerostar I bought some stuff from an auto glass place locally- and it dried differently. The stuff that Ford uses will remain pliable for life.
To remove the window is easier than you think. Remove the interior trim and you will see nuts around the outside of the window frame. Remove those nuts except for a couple on one side which should be loosened as much as possible. Then push hard on the opposite side of the window. Heavy continuous pressure will loosen the window from the sealant- don't loosen it far enough so that the studs are outside the body of the car- the window might fall off when you remove the retaining nuts. You just need to loosen it enough to remove it from the outside. I would loosen it all the way around the window before removing the retaining nuts. Make sure the window is resting on the studs before you move to the outside to remove it. If you have help, then someone can hold the window on the outside. I never have help, so this is how to do it alone.
The sealant will still be sticky and rubbery. You must remove all the old sealant before using new sealant to seal the window. If found it was easy to ball up the old sealant and use it to stick to what was stuck on the window. The stuff Ford uses removes fairly easily. If it doesn't come off easily you can use a plastic putty knife to help loosen it.
Apply the new sealant liberally. One tube was enough to do more than one window on my Aerostar, so gob it on like crazy for a single Focus window. I'd use a bead about 3/8" wide on the car, then place the window over it. It might be prudent to apply some painter's tape to the outside edge of the window where excess sealant would be seen after the window is installed. The inside of the window trim should be curved to push excess sealant to the inside- sealant around the nuts on the inside is ok, the interior trim should cover it.
Wear laytex gloves while installing. This stuff doesn't clean up easily. I don't even know if the painters tape idea will help you if you get too much sealant under the window, but with painters tape and a plastic putty knife you should be able to trim the excess before it dries.
Let's hope you don't have to do the window fix. There is a trick for testing weatherstrip with chalk to be sure it is sealing completely that you might want to try. Home Depot or Lowes sells powdered chalk in a plastic tube for chalk lines that you can use to coat one side of the weatherstripping on a door, then close the door and see if the chalk is transferred uniformly to the other side.
I do think the window is it though since the door openings are designed to drain away from the inside of the car- door weatherstrip is usually only to blame for wind noise.
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