Personally, I would probably try to make a straighter version of the stained glass. It looks like an old window & often with stained glass repair, the welding repair results in the metal frames becoming slightly larger. Over the years, it builds up creating an irregular shape.
I love all the ideas everyone here has suggested. One other option would be to do it reverse applique. I think a piece of black felted wool on the top with bright breezy batiks peeking through could well represent the stained glass & account for the irregular shapes. I agree with Lizzy that making a paper pattern & transferring that to your black fabric would help regardless of which method you use.