Nice stuff, Jeff.
I don't think there's any way of adding captions, or any kind of reference number, to photos in a photo grid. It's something Adobe have said they are thinking about adding.
As you observe, you can't control the order of images in a grid either. Nor can you change the cover photo for a collection, as far as I can tell, without deleting it from the Portfolio site and reinstalling it.
Portfolio is easy to use but, I find, incredibly frustrating to tailor. But it's worth every penny I don't pay for it.
Jeremy