Chris,
Great looking diagrams. There is so much to see that making it all work 100% will probably develop as you actually wire it.
I don't know how detailed your diagram was, but I have a few questions/thoughts.
Your alternator wiring shows the larger gauge wire going to a fused feed from the ignition switch. The two wires terminating in the DA plug would be marked #1 & #2. Number one would be a smaller gauge, and this is the wired that needs to be switched. This same wire could also go through your little lamp to provide a resistance, AND act as your 'idiot light'...or battery light as you have it noted.
Wire number two from the DA plug would be the larger gauge, and could actually wrap right around and tie into the large BATT terminal.
With all the cool stuff going on with this rig, a nice single wire alternator would eliminate some wires. A internally resisted coil could dump a few wires too!
If you installed one or two firewall mounted power blocks, you could tie your your alternator output to the battery there, as well as a hefty feed for the fan relay.
You have lots of things going on, and it sure looks like you will have fun wiring it, especially with the nice 'blueprints' you have drawn. Good luck.
Stuart