Here is the quick sketch:

One quick correction. North and Nevins Yards should be flipped. Nevins runs parallel to the mainline.
These are my goals:
Model the dual track Conrail mainline between the P&W interchange in Worcester and South Station in Boston as faithful to the 1998 prototype as possible.
Worcester, Framingham North, Nevins and Beacon Park yards are needed as well as the South Station passenger terminal.
Return loops off the P&W interchange and Grand Junction at Beacon Park for continuous operation.
Full scale models of South Station, Fenway Park trackside complete with adjacent operating Citgo sign.
Full scale Worcester Station.
One thing I am not sure is what to do with grades. The Boston line inclines 1000' as it travels the 50+ miles to Worcester. But this is mostly after Framingham. Hills are not a big part of the scenery until you hit Worcester. Due to a sump pump enclosure near the Boston end, the layout has to start at least 51" high. I don't know if I should model the grade at all since it is so gradual and I am starting at such a height.
Stuff I would really like to include:
Westboro Yard and industries.
Loop to hidden staging from the end of North Yard.
Addition of Framingham South yard for autorack operations or at least a branch to hidden staging.
Addition of the branch to Walpole/Canton from Framingham (also hidden staging)
Addition of the Ayer Guilford/P&W branch from Worcester (hidden staging)
Interchange with Grafton & Upton in North Grafton (shouldn't be hard - its a freight house and concrete plant)
I want to keep the layout along the walls with minimal peninsulas if possible. I want a wide area to stretch out in.
Will need to add a lift out bridge to connect Boston to the rest of the layout - exterior door breaks up the south wall.
The layout is scenery first, ops second. I don't want it over crowded. It needs to bleed the prototype. Lance Mindheim's Monon, with its huge scenery-to-rail ratio is exactly what I'm looking to do.
Another idea I was thinking about is a series of small layouts set into large bookcases. Each point of interest would be modeled as its own diorama, linked with hidden trackage. Think of the model railroad version of this:

and

This would eliminate that compressed yard-next-to-yard look. It would also make lighting REALLY easy. Building additional walls and floor to ceiling bench work looks a bit daunting though. And I'm a bit terrified of all that hidden trackage it would require, unless I made the dead space between dioramas removable panels.