Okay...as of now, the Mongoose Salvage Co. has removed all of the rail, redstone torches, and buttons associated with the main Netherrail line, and placed them in their requisite chests in the storehouse. (I might go back and grab the fencing separating the two rails later, since the storehouse doesn't have much of that.) I didn't touch any of the signage, so it's still useful as a shortcut until the Nether's reset. If anyone still needed to use the rail on a regular basis, I'll gladly pull a mea culpa and re-lay it. I left the loop to the portal to Sara's floating island, since I assumed that was her own material. I also left the loop from the locked "library" door to another portal, since I have no idea who owns that. I'm assuming it's whoever made the great little "Your Ad Here" sign next to that huge circular...whatever it is. It's an awesome thing, albeit rather infested with Endermen at the moment. 
Oh, and if anyone is ever in need of wood, wheat, melons, or mushrooms, just let me know and I'll hit you up. Come to think of it, I should toss some melon seeds in the storehouse, since I have more of them than I know what to do with.
Thanks for doing that. I was planning on doing it myself but I got caught up in the 1.0.0 launch frenzy and had updated before I had realised and with other things occupying my time (Skyward Sword, Dorf Fortress, coding, life, etc.) I haven't had the chance to downgrade yet.
Anybody have any idea how I can prevent pigzombies from spawning on the tracks when I rebuild? As some of you have seen I have been experimenting with combinations of blocks and fences to try and stop them but they still popped up from time to time and I want to get it right when I rebuild the network in 1.0.x.
Also... it might be a good idea for those with portals who want them linking back up to the new network to post their overworld X/Y/Z/F co-ordinates so I can manually rebuild the nether side ones to ensure we don't get as much conflicting as we did before. Also say if you want a station, built-up or just left exposed. I'll have creative access so I might as well make use of it.

If any of the new nether structures get in the way of the network I'll do my best to go around and even add a access station but if it looks like it will look good I will break in and build through unless anybody has any objections.
Once I have the basic layout done and tracks laid I will give up creative mode and return to my life of strip mining to continue it's expansion.