In addition to Gary's comments, if you have an inkjet, you need a transparency suitable for use with an ink-jet printer - they have a special coating on one side to allow the ink to stay on the plastic.
Many churches have their windows protected by wire mesh or clear plastic to prevent damage by vandels. These often obscure the window detail completely from the outside and could save you time.
Another way to produce stained glass is to photograph actual windows with colour slide film and put several frames together to form a single window.
Have fun!
John Webb