Kevin, I just ran some more simulations and found that once a train goes down to the yard in either direction and comes out, it cannot go down again. I don't know why I didn't noticed that before, but I made the changes outlined in Red. I deleted the turnout on the right and the tracks running from it. I then added the turnout on the bottom. This doesn't solve the steep grade problem, but at least you can enter/exit the yard and get back to it. This version is from before I moved the crossover further around the curve. I only offer the photo to show how it needs to be connected to the main in order for things to work properly. I also tried moving the bridge and having things cross in a different location, but nothing I tried fixes the grade problem. I think you might want to try unfolding the mains to run around the perimeter with the RH/TT moved toward the lower right corner. I don't have time to try that tonight and I'm busy part of the day tomorrow, but I'll see what I can do later.
As far as what I'd do with a clean slate, I doubt I'm the one to ask. I'm more into just running trains, not operating a model railroad, though if I had this much space I'd probably start with a double main running the perimeter, raise at least one of them along the right side around to the left and place the bridge on it going across a canyon or something. Having the RH/TT, I'd probably make a nice "operational" yard a feature of the main level, not hidden. IMHO, even if you don't move cars around in the yard, it will be a little strange to have the RH/TT without a visible yard.
