The game does have 3D rules; they’s long and annoying, and mostly given in William’s answer. I’m not at all clear what more you want.
Personally, I despise these 3D rules: they’re difficult and time-consuming to use, because there’s no good way to indicate 3D area-effects, calculating distances moved involves Pythagoras and marking the paths used is impossible, and so on. They represent a bizarre and considerable increase in the amount of simulation that the system offers: at the same time that all of the maneuvering and positioning and lunging of combat is abstracted to a five-foot square, you have flight speeds that have turning radii, minimum forward movements, different speeds for up and down, and the aforementioned necessity for using the Pythagorean forumula to figure out the diagonals. These are details that I do not think the game needs in the slightest; they are way more detailed than most other aspects of the game. I want an epic fight against a dragon, not an incredible dragon-flight simulator.
I dislike these rules so much, in fact, that I have written houserules to eliminate most of them altogether. There are still nods to the differences in speeds for going up and down, and I do use the minimum forward speeds and turning radii since otherwise the maneuverability ratings wouldn’t mean anything. But flying or not is just a “status condition” that changes how you interact with, say, difficult terrain, and whether or not people can melee you or vice versa. It eliminates all need to figure out 3D distances or shapes, and is therefore, in my opinion, massively superior.
Just an alternative for your consideration.