Wyatt, here was my thought on your arrangement. This is similar to a friends layout and their setup is very close to yours.
Larger image at
http://picasaweb.google.com/lh/photo/b3w3JMj1kXftkgVxHF0-WA?feat=directlinkBasically, the helix on the peninsula allows for the transition between the 1st and second levels and from the second level to staging below the 1st deck. The other helix just goes between the first deck and staging. Shelves along the wall are 18", which could be dropped lower, and all aisles are 36", except for the 30" squeeze points around the helix. The peninsula "shelves" are about 13" wide but those could be enlarged if the shelves around the outside are reduced. On the first level, you'd have an industrial spur on the other side of the peninsula after the main has entered the helix. The helix radii are 18",
Phil