Matt,
I think your plan looks good for your goals at this time. Run 3 or 4 trains at a time, and you can easily change things around when you are more settled in. I have no worries about you making use of the access hatches you have included. By the looks of your avatar photograph, you are young and flexible like I once was. I wouldn't go for access hatches now on my layout, but you will be fine.
Yes, I know there are folks here who can recommend the right upper level supports like the Chicago EL.