Sorry to hear one of the pups died. I would remove them to a system of their own. You may be right on the feeding/water changed schedule is too much for them. Does the pup tank have its own filter as well? Or just flow through from the pond?
I wouldn't leave any food in with them over night either. I would feed them small amounts a few times a day, making sure everything was eaten.
Don't think it was the guppys either, especially where you've had them for awhile.
You are doing a great job! You should change your user name to Marble Master