Obviously, I'm fully aware that levels 1 & 2 are basically just 2 ovals folded over to form the 4 mains at the tunnel. I'm also aware that the line coming off the wye is also just another oval folded over. What I wasn't aware of (and still might not be) is how much you're willing to alter the design in order to make room for the 2 levels below the main level, how acceptable it is for the line off the wye to be lower than the mains going into the tunnel and how much space you have for the changes. While you might think it's easy to change the curve on the left so the spur lines clear Level 2, it's not apparent to me how much room you have to do that. Still, I took the time to see what it would take and here's the result. Mind you, there is still a lot of work for you to do the make sure the spacing between tracks is wide enough for trains to pass and you still have to add the other mains plus the yards, etc., but this should give you a good start. Make a note that the black turn outs are simply a straight and a curve set to look like turnouts to get the grades done., The real turnouts that would go there are off to the side.
