A while ago I created a simple template godot project with things like a menu, pause screen, simple saving, etc. Can I use it or does everything have to be made in the three hours? (Btw in the title I said assets, it doesn’t actually have any gameplay assets like a character or anything)

You mean assets... off the shelf? Sorry, couldn't resist. Anyway, on overview page it says that

Using pre-made assets is no problem, just make sure that you have the necessary rights to use them, and attribute them in your game’s description properly

I've also used template project with aforementioned functionality in past jams. I think generic template project it fits the description. IMHO 3 hours is better used developing the game itself. As a disclaimer this is just my take on rules, I'm not associated with jam hosts.