Jeff, just some food for thought. I don't think there's a way to do what you want in the new space, so I played around a bit.
I played with several versions of a yard to fit your peninsula and the one of the far right offers the most storage. However, they all suffer from the closeness of the turnouts, so storage is less than what's shown. Note the 4.8% grade to get down tot he lower level and be able to go under the upper level track. It'd be a little less than that because I have it going from 7.5" down to 0" when it actually only needs to go to 1"-1.5". The point is it's probably going to be steeper than you want. I also don't know how you expect to go down to passenger tracks and then get back up, so I decided to see what kind of yard I could fit on the lower left.
This removes the peninsula, changes the inner loop to O-72, puts the station above the siding and keeps the yard. I see no way to connect the blue and orange tracks.
