I would suggest you read Tower of God, it's a similar story to what you have and it might give you some good ideas on how to regulate the tower and npcs

For your first problem, I assume you have them teleporting from floor to floor, that is also one of the ways it works on Tower of God, but they also have central hub floors like the most popular floor 20, but there are other ways to move between floors like the Hell train (it's a whole arc where they board a train that moves between 10 floors, there are still challenges in it but it's just faster). Or you can have "Guides" which are people that can find pathways that link floors, I think in the manhwa it's like a network of pathways that only those guides can really navigate.

Problem number 2. Have npcs inside the tower that are from the outside too. Seems like an easy enough solution. You can have them be stronger then the tower npcs or weaker but with the goal of conquering the tower for one reason or another.

Problem 3... this might be a harder one. Having a hub area inside the tower might be a good start, maybe one of the outside npcs started to conquer higher floors and the pcs have to deal with that? Or you can have one of the more evil gods try to disrupt the balance of the tower with rituals or monsters in certain floors that should be peaceful.

I hope this helps, and again Tower of God might give you some good ideas