Old Prof - I was hoping to hear from you. I have some news - there is finalized version of the Bergen that has been out for the past 10 days. Give it a go and read my notes. The route name is New York Division - Croxton Ordinary.
Regarding the Operations guide:
1. Its a scaled down version of the real employee manual for the New York Division: the take away from the first section is basic track rules and speeds and list of "stations" which becomes really important in the Builders Section.
2. The consignee list - This is the overwhelming section. To simplify it, Separate out Carlton Hill (as the sidings are not built yet) and the Ford Plant (as it so large operations center on it) The rest is a list of the other 47 consignees and what they take. EDIT: The key thing is the FROM and TO STATION at the bottom of each entry. Correspond the stations to the markers on the route - you can see the traffic flow!
3. The Builders Section: your most important take away ( and what I learned ) is the concept of freight "stations" Here are the 4 basic operations of our freight line.
A. Through Freight Points West or East that start or end at Croxton.
B. Station jobs: Full cars are delivered from Croxton to yards, interchanges and sidings. Empties are picked up form yards, interchanges and sidings.
C. Locals jobs: Full cars are picked up from stations and delivered to customers, empty cars are picked up and delivered to the stations.
D. Yard Jobs: classification and the building or breaking down of Through Freights and Station Jobs.
When you combine the Consignee List and the Builders Section - you get the make up of your yards and trains. The first thing you will observe is that we have a majority of cars that are covered hoppers! This will be repeated over and over.
You will notice the smallest amount of traffic is cars originating form customers to be delivered outside the railroad - just like the real thing.
The information there is a GUIDE and not a RULE. You will find that by reading it, you can now visualize the traffic, it starts to make sense. Width all this data you can present classification jobs (which are hugely boring to most) with a degree of realism that will make sorting interesting and you can identify not only what specific customer but the amazing detail of the load itself, which your conductor would see on his manifest.
I haven't tested it yet, but I really believe this is going to work they way I have outlined. Now if I can get the kids to wrap their brains around this... then we would have done something !

EDIT:
Perhaps it's too late, but I'm going to suggest anyway that you avoid placing full-length markers on sidings or stub tracks. Short markers that identify the track's purpose (e.g., "Classification 1" or "Z-brand 1") placed in that area very close to switch frogs where freight cars would not be left are best, since they allow scenario writers more freedom.
- I am still digesting this ... interesting