Got any plans yet James?

I think the area you're considering is great, but I think something patterned after Brooklyn Yard is too much for your space. You really need to narrow your "Givens & Druthers" a bit more, especially operations-wise. The Pike City plan seems to be about the right scope for your space, though I would highly recommend some form of movable track for mainline runs.
Have you considered something iconic like Portland Union station and the Steel Bridge over the Willamette? The wye on the other side of the river offers a great entre to terminal ops and mainline running, and the river makes a perfect aisle. I haven't quite figured out a way to make it work in your space with the wye, but topologically, I was thinking of something like: (in vintage ASCII art!)
Brooklyn
____________________
/ \/ \
| |S.B. |
| | |
\______________/ / to staging under P.U.S.
P.U.S.
The top is some industrial portion of Brooklyn, the bottom is Union Station, the middle vertical is the Steel Bridge feeding a wye on top, the right vertical loops back to staging under P.U.S., and the left vertical is a temporary track over your desk and across the cupboard and door for roundy-roundy. It could either hook up to PUS, or to the staging underneath. The latter would be more prototypical for N-S mainline running. Both top & bottom stretches could feature riverfront scenes.
If the concept appeals, the challenge will be to make it fit...
-Gary