I think the way out of the cycle here is that your equations are not specifying the universe, they are merely describing patterns in the universe. So we model the universe with numbers, which are based on set theory, which like numbers is a product of our mind, which is a structure that exists in space and time.

It is helpful, I think, to think of numbers, sets, and the like, not as anything fundamental but as tools that help us make sense of the world.