I feel like up until yesterday or today, my custom rewards were above the item store. I am interested in using HabitRPG in a way that really prioritizes the custom rewards. Is it possible to swap them again so that the custom rewards are above the store?
No, I'm afraid there isn't an option for that. It was changed to assist with improving the tutorial for new users - for reasons I'm not aware of, it was necessary to move the Rewards down.
I'd encourage you to suggest an option to move them back up. You can do that from the Help menu - select "Request a Feature". If you find that there's already a feature request, you can vote for it to show that it's more popular.