Thanks, Peter, it is interesting to see how these ideas play out. Fastrack has a pretty decent selection of pieces to work with (no flextrack of course), but I wish Lionel would add a #5 or #6 turnout, and O-84 1/3 section (7.5 degrees).
For this design, I had to ensure that there was sufficient vertical clearance for the hidden track in the tunnels. So I placed the hidden track so that it would NOT be directly beneath the lines running above. Then, I only had to make sure there was sufficient vertical clearance where the lines crossed (including the spur at the bottom which crosses over the mainline beneath). I added elevation and grade markers to this image:
