I did this kind of work for the Sacred Landmarks Research Group here in Ohio, and further researched, photographed, and wrote a paper when the Catholic Church began to document the glass in churches.
At that time, I was shooting and scanning, both with slide and color negative film. At the end, I was using color negative 35mm as it had latitude in exposure, and the processor would just scan the whole roll to Hi Res Tiffs and burn a CD for me as the film came out of the C41.
Are you trying to document the glass, or going for something with aesthetic appeal?
Last trip out, I used a Nikon SLR and a Cosina RF with a 12mm lens for the tight shots.
I used Photoshop's corrections for distortion in the windows I could not shoot straight on.
Exposure wise, I used a spot meter and picked out several middle value pieces of glass to place the exposure.
If the window fills the frame, your in camera meter should handle it adequately.
One thing, scanning MF is expensive unless you do it yourself, and the file sizes will be huge-- so you need a significant computer to handle them.
I shot an entire church with a 105mm on a Nikon, but that tells you something about the size and layout of the 100 yr. old Catholic church, which was later burned/torn down.
Church said they were in the Church business, not Landmark/monument business.
Even on a cloudy day, you will have plenty of light. If the light is hitting it directly, you will get some flare. You could do a walk through with a spot meter to see what you have, but they are windows and are designed to be seen.
For printing "book size" you do not need MF quality, but if I were shooting MF, since they are just about giving away Mamiya 645's, I would use that for the choice of glass and the SLR view.
You can also adapt inexpensive Jena lenses to it, and I think I could give you a good price on the 50mm shift lens I have somewhere for it. ;-) The Russian fish eye is a hoot on it.
Regards, John