New to track planning...suggestions/critiques?

Here's a new version of my first layout. I work with at-risk teens and am close to finding a sponsor for this project. I switched from MTH Real trax to Alas O. I like MTH Scale trax but want a larger third rail as all my locos are third rail (NYC S-2s, P-2s (require 72 curves) and commuter MUs, as well as NH EP-5s, and commuter MUs. In addition I didn't like the toy like quality of the MTH Real trax. I still haven't mastered grades and heights so they are not done in these drawings. Would love some feedback in terms of the operational aspect of the design from some of you more seasoned model railroaders, as well as some advice on what I should do for grades and clerances necessary to accommodate the trains for under the terminal, considering the bench work may be an inch thick (?). What would be some good parameters to shoot for?  I've put the original drawing as well as the lower levels and the anyrail files. This is one of seven very different designs and the only one with significant freight possibilities I'm sure many of you will recognize it from an article that was in Model Railroader a while back.  All advice and critiques will be valued as I'm new to this.