Ken- l love the creative process you're going through. Thanks for sharing with us.
A few thoughts- keep the run around tracks and sidings. You can't have too many in my opinion.
Can you shift the bridges to the left and just use module 5 as a swing out instead of both?
I bought a great telescoping attic ladder from Werner several years back. It's more compact than a traditional type and works great.
I think the two car garage idea with the trains upstairs may be a winner (assuming you need a garage too).
I would look at conventional construction over a kit as well. Talk to some local contractors for their thoughts.