I have a 2001 Custom. I put a Mustang on it. It is the large one, a wide super touring. I can ride all day without any discomfort. I also have saddlebags and a windshield so the seat does not look out of place. If I was stock, I would probably go with a standard size Mustang.
I received the Mustang Sport Touring seat (#75733) and put it on my '03 1200S three or four days ago. It's truly outstanding......all the difference in to world, both front and rear, and looks good. Best money I've spent so far.