I don't think skyrails would be a good idea, the admins might take it down. Maybe you can put the rails on the ground but make them follow the terrain, like warlord said
Maybe we can make 1 lvl like 5 blocks above sea lvl and just put ot on stilts ( fences) and have go through mountains and things. The reason I say this is because following the terrain would not be as smooth idk I could build a few "test" tracks and see which one looks and works better b4 we decide
Yard I would like to be involved in the construction of this if possible. I think the best idea would be to make it like an actual rail way, what I mean is it will follow the ground but will be limited in the grade it can climb, for example, lets say it can only raise up one block for every 4 blocks of travel, if a grade or hill is too steep then a tunnel or bridge would be required. This will give the track a nicer look in game and on the dynmap, but wont limit the rail to be completely flat and completely straight. I have also been doing some research into automatic railway systems since we were going to continue to expand our current railway to include one, if you interested and anymore ideas I have tons.
As far as the warps go, I think that the purchased warps/VIP warps should stay, because people earned those, and they can be helpful (and also give more reason to donate). However, other warps/the portals could go.
Just as a side note to Yard, in relation to minecraft physics, you can make 45 degree turns on a minecart track and only lose a mild amount of inertia, thus making a minecart line much more feasible when trying to guide around terrain features.