The Ford Transit Van Window utilizes the factory metal stamping, on the interior of the van you will notice an area where the inner metal ends. Here is a photo to clarify. You will cut right along that edge all the way around your van may have multiple upright you will cut those out straight with your opening.
If you are replacing an existing factory window that glued in you may want to take to a professional for removal and replacement. Best tool to use is a wire cutter Equalizer Window Cut-Out Set. Once the window is cut out you will need to cut the original urethane down as flat as possible and clean as much away as you can CRL Adhesive Cleaner.
Once the Hole has been custom out or window removed its time to install the new window clean the outside metal of the van with rubbing alcohol or PWR22 Cleaner this will insure a good hold of the urethane eliminating contaminants.
Using a urethane primer apply to the outside of the body you want to be close to the opening but allow a 1/2" of gap when possible as when the urethane is applied it will spread and you do not want to urethane seeping out on either end as its very tedious to clean. Allow primer to dry for about 10 mins, now you can apply your urethane, most of the urethane will come with a v-notch or an etch for a v-notch in the tip this allows for a nice large bead of silicone make sure you evenly distribute to urethane to not have hitch or low points when changing urethane overlap the existing bead slightly to insure there will be no gaps.
When placing the window you want to get it as close to desired location as possible one in place you will have some wiggle remove to get it lined up just perfect one you have it where you want with an open hand pat all the way around the window where the urethane bead is to get a good solid hold. Using Window securing tape , tape the window in place. You will be able to drive your Van after 3 hrs and remove you tape after 24hrs, best to wait 72hrs before washing vehicle.