Andrew:
I really like your ideas. I haven't given much thought to actually using a prototype railroad for drawing ideas from, I was going totally free-lanced. But looking at the Modesto and Empire Traction Company site, I have had my eyes opened. I can still freelance but get a ton of ideas from that site. Thank you for giving me the info.
I know, I know, what I really need to do is find a club here in Houston and go attend some operating sessions so I know what the heck I am doing and what I want before I build, but don't know if I will take the time to do that... instead I will just jump in head over heels and build the layout and everyone can say "I told you so" later after I make a ton of mistakes.

ops:
Edit: WARNING... I was confused when I wrote the following:
Question: If I put an interchange at a couple of the industrial areas, would I still want the staging tracks down at the bottom right of the layout? Or would the interchange tracks be the source of all the cars coming from "off the layout"?
My previous thoughts were to use the staging as a source of cars from interchanges with other railroads. I see that your idea opens another huge source of moving cars around and making up trains by switching on the layout instead of just making up the trains by hand on the staging tracks.
End of confusion^
The helix would certainly make constructing the rest of the layout easier instead of having all the different grades along the mainline. But I am a bit scared to take on the helix, have heard bad things about them. Would 22 inch radius resulting in 2 3/4" difference be difficult for an engine to pull 12 cars up? And if it couldn't, splitting the train and pulling twice would be acceptable? Perhaps even a source of more operations?
Also, is the 2 3/4" enough clearance to pass under for the next loop?
Ugh, sometimes I think I am getting in over my head! Possibly more research is needed before I jump into this?
and I was wanting to start on the benchwork tomorrow...