I think your right that I over proofed them. Since the two recipes have different proof times, waiting for water take for ever to boil, etc, led to longer proof. Next time I would probably just stick to trying one recipe at once not two different at a time.

I have tried overnight pizza and that worked well. For bagels do you recommend proofing the whole dough in the fridge or when they are in their "bagel shaped" dough?