You need:
9mm socket + wrench
a tool to clean of the butly tape used by ford to seal the window in. Don't worry, if its the seal from the factory, it will be crumbling by now.
A tube of windshield urethane
Some black metal primer, or whatever color.
A razor knife (preferably the long handled ones "long knife")
A LOT OF TIME
Okay, here are the steps. First, vacuum up all the glass you see, because even tempered glass will still cut you, and pokes like a bitch.
Then, remove the rear inside large plastic 1/4 panel. (have fun with this one)
Once removed, you should see a bunch of 9mm brass looking nuts that follow the perimeter of the window. Undo them all and save the nuts.
Once they are all out, take your razor knife (be careful here) and insert the blade in between the body and the remaining rubber trim of the glass, and lightly pull it along the perimeter. This is to cut the butyl tape. (Try pushing the window frame first, it may just pull right out.)
Now, once the window is out, clean off ALL the leftover crap, as much as you can. Take it down to bare metal if you need to. Once clean, PRIME PRIME PRIME any scratch marks. This will prevent rust, and trust me, it will rust if you miss a spot.
Prep the new glass. The bead of glue will be run right where the old butyl tape was, so you can see where it will hit on the glass. Prep the glass with some rubbing alcohol (we use a special solvent, but alcohol works) along the line where the glue will hit and let it dry.
Run a bead of the urethane. DO NOT run it any thicker then your middle finger, as you will just have a huge mess. For that window, a bead about the size of your pinky the whole way around will do.
Push the window in, it lines right up as the threads line up with the holes on the car. Once it is in and slightly pushed down, Start rebolting the window to the car. Torque them evenly, like you would changing a tire.
No high pressure car washes for 24 hours afterward, just to allow the glue to fully set.
Any other questions, feel free to PM me. I'm an autoglass tech if you couldn't tell.