The F7 and Mikado should be acceptable and no more than 50' passenger cars... maybe the walthers trainline 60'ers.
If you can live with a few inches or more of seperation between the tracks on the grade, I think you will be more happy instead of one ramp down and one ramp up parking garage style.
The location of the flyover is going to cut into your operating pit. You want to keep your tracks within 2.5 feet of your reach at all times otherwise there will be a problem if .. uhh.. when a derail should happen.
Your ideas can work, but you don't have a great deal of room to get the clearances you'll want unless you are willing to also reduce the lower main at the overpasses. It would help if you would draw separate diagrams for each level and flesh them out a bit.
I also agree that you need a cross-over along that tight parallel section at the top of the diagram just so that you can change the direction of travel......even if only once a week.
Chip is right about the scenery issues if your tracks are at disparate levels and close together; the embankments become a real headache and you will find yourself relegated to pretty much retaining walls....many hundreds of scale yards of retaining walls, or rock cuts.
Nothing wrong with your choices of curve radii, as long as you accept firmly from the outset that you limit what you can get to run on the trackplan. In fact, it is probably best to set these limits and to not let them become impediments to your overall enjoyment over time. Many's the layout that has been reduced to rubble because it didn't have any legs...it didn't have an room for growth planned into it. I often counsel new builders to understand that they will very likely want to keep acquiring new locomotives and rolling stock, but they find later that they can't run these new, usually large, items on tight curves....their curves.
You are going to want to reverse that train. Round and round that a-way and time to return to the yard and no way of getting there except swapping caboose for engine and backing tender first to it.
Better just to have it one level and have a small double ended yard on the longest side and a town on the other for some switching. A view block or some sort of variety in your scenes will help.
One good passing siding can be put on the yard, save the short runaround for the town local.
I agree with Chip.
It's very tempting to try to double your run by going up and over, but in the end it requires considerable grades (even 2% is a big deal) and vertical scenery which is awkward at best.
I did one of those types of layouts, but watching the train traverse the same scene twice, on different tracks, seemed unrealistic to me.
Railroad yards not withstanding, most of the time we see a small track in a very large scene. In other words, as long as they're arranged such to maximize operating interest, often times less track is better.
Modeling the Rio Grande Southern First District circa 1938-1946 in HOn3.
Chip
Building the Rock Ridge Railroad with the slowest construction crew west of the Pecos.