QuiltE

I like it the way it is ... while I see your idea of making it more stained glass like, I would have the fear that it might take away from the effects you have going with all the colours. The way it is pieced now, it has a good sense of that stained glass already. Of course, I am somewhat guessing as we have no perspective as to the true size of each of the pieces, or the overall piece.

Are all the different colours/fabrics sewn together? Or have you done it with a fusible?

For the cross, I would stick with a bright white, keeping with the traditional look. I'd make sure it is a solid fabric, either on it's own or with a backing to ensure it does not let the colours under it show thru. Some of that might be sorted out, in how you choose to attach the cross.

My visions for the border, would be a royal purple with a yellow/gold inset flange. Again, colours that have religious significance. Audition a few things and see what looks the best.

Backing ... could be most anything!
You could keep with the purple or any colour or print you choose.

Depending on what sense of humour your DGS has, you might choose something totally unexpected ... is there something else in which he has an interest and even passion? Perhaps his favourite sport? cars? etc. I make this suggestion as a good friend of mine is a Minister. When she was ordained, she received the serious religious things, but also appreciated those which spoke to her sense of humour ... and that has made her a much-loved Minister to any who have come to know her.

He's going to be quite impressed at what you have created for him!