Wow! Lots of feedback! Thank you everyone! Thank you Dave for the different designs!
I think Dave showed that the wye is pretty much out. It may fit, but there would be S curves, one loop completely under the other (which might be a okay) but I'm thinking it won't work well.
On the yard peninsula being parallel, I only see aisles about 18" wide. That could be extended a couple inches here or there, but much too narrow for the long run. I plan to store things under the layout. I may need to roll a chair in someday in the future.
The angled yard makes larger aisles, but one pinches down to a point. That may be more workable actually.
Now to the yard on the main shelf between the two mainline tracks. Dave got it to fit in 30 inches. There aren't as many tracks, but they can be longer. That isn't bad.
I think I am going to have to ponder this some more. As was expected, none of the scenarios will be perfect. Each will have a drawback.
Here is an idea someone emailed me about. He sent me a hand drawn .pdf. I doctored up an earlier design just enough to show the basic concept. I know there are lots of gaps. He is using this concept on his layout and I have seen others do it. Instead of the end loops going through switches to single track mainline. He showed what is in effect a double mainline. He likes that because he can run two trains independently with a longer run. It is a good concept, but as I told him it goes against my desire to depict the prototype. I'll through my chicken scratches out to stir the pot. 
