Well, after many hours of plotting points and creating a config file, I think I have a pretty good 3d layout. It lets you see a large portion of hosts from one vantage point, and you can simply rotate around it to see the rest. I basically created a 2D layer that I repeat over and over again; you just keep using the same set of XZ coordinates and change the Y coordniate when you work back around to the position you started with. This map is in the shape of an octagonal tube:
I have attached a config file that you can use as a template. Just replace your 3d_coords value with the ones in the file and increment the middle (Z) value by 1 every time you start a new layer.