I believe the central spawn portal, and the road connecting it to therother and my place, is at about y=46. It originally spawned higher, but we submerged it to avoid problems with ghasts in the central network area. The road itself is mostly in the open, it's just the immediate area around the central portal that is underground.
You can also move your portals anywhere you want vertically without impacting anything. Unless you've got two portals on top of one another, the y coordinates don't make a difference. So, you could move your nether portal much further down.
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