#2 I think it would be cool to make the hub out of obsidian and the tracks out of cobble/glass. There are obsidian generators that convert redstone to obsidian they make mining much safer.
#1 & 12 With your figures I figure we should have a portal every 128 nether blocks. Minecarts travel well with a power rail between every 32 blocks. Combining that we could have a portal every 4 powered rails. Our world border is currently set at 7,500 blocks from spawn. That would only give us the need for 6 portals going each direction to cover the full distance North/South and East/West. All we would need after that is a beltway or two that would cover the NE, SE, SW and NW parts of the map.
#11 I feel a travel system below the bedrock but above the majority of the nether would be the best place for the travel network. I see it this way because then the networks serves multiple purposes for users of both worlds. Whereas a network above the nether would only help the overworld.
Public teleports starting with res tp are public because the res owner made them so by setting the residence tp flag. This is done in two steps first typing /res set ResName tp true. To set the location where people would warp in first stand and look where you would want them to load as and type /res tpset