Two things to keep in mind: a) this IS a major undertaking and once begun not easily reversed & b) none of us here have done this more than a few times at the absolute most. What you have in bits and pieces is collected knowledge along with many helpful ideas formed as much from learning what NOT to do as any other way.
With a bit of pre-planning this process is straight forward and simple for the most part---you're simply cutting a hole and screwing something together. As with anything else the details are vitally important----so far you've got the basic idea in mind which will serve you well.
CarringB contributed this link from Ford:
https://www.fleet.ford.com/truckbbas/topics/incomp.html Go to that manual, find your van year (or within a year or two either way) then scroll down to find the pages addressing "body panel window removal" (typically about halfway thru the entire file) and read carefully about where to cut.
Most good brands of aftermarket windows are sized to fit into the factory approved areas like those the Club Wagon uses. You don't want to cut into any of the vertical structural sections that run from floor to roof---you'll greatly compromise the body strength. Careful reading of the manual in the link above PLUS looking at a Club Wagon will give you a better idea what's possible.
IF you're able to see a Club Wagon with the interior removed all this makes perfect sense. Don't look at an aftermarket conversion as a guide though---some weren't done correctly. Factory only OR a member here who has complied with the best practices as outlined in the manual.
Most any autoglass shop would gladly sell you a CRL window if you specify you'll be installing it yourself. I've priced a few for another member here, was under the assumption I enjoyed a decent discount but for E-Series windows I have no advantage what so ever. Shipping is another consideration so your distance from one of CRL's warehouses figures greatly into the final price.
Additionally windows may or may not interchange between brands so that's another consideration. This link to CRL's full line of van windows is where you'll begin---look for the models fitting your year and brand:
http://www.crlaurence.com/apps/sites...y=Van%20Window
If I can be of any help please feel free to PM me.