I took some more time with version 2 to fix the geometry, and utilize some turnouts I already had, mainly #11's, in place of the O64's that were used on the 2nd level track. I've been pondering over several iterations of my prior designs for at least a good solid month, but was never completely settled on it having what I wanted. Since I've gotten over the whole "don't cross the entrance" idea, it's really helped cleanup the layout, add some good straight sections, and really add the space for scenics I was wanting. In this revision, I moved one of the 2nd level crossovers to the east wall, so I have an uninterrupted straight section right where my aisle entrance will be, which should make a swing out, or lift out section much easier.
My 2nd level will probably be about 10" higher than the first level to allow me to place buildings and industries under it in sections, or creatively use cut-aways. At this point I suppose, I'm looking for glaring issues.