Okay RD, I see where you're coming from, so I'll try again to see if I can explain things a little better.
You stated that the 4 mains and the line with the wye were at the same height coming up from beneath Level 1 where the crossover with the turntable line is (yellow rectangle). Therefore, THAT part of the grade (black dot to blue dot) gets the track for the Level 3 down to the 34" point.
However, because there is also a return loop on Level 2 (blue), Level 3 has to go below it. In order to do that, it has to go down another 6" to the 28" point. And it has to clear Level 2 at the point where they will cross (cyan rectangle). I did error in that I initially said they crossed where the red rectangle is, but they actually cross earlier where the cyan rectangle is and that makes things even worse.
Now, I temporarily replaced the turnout with an O72 curve so RRT will let me create the needed grades. Because the grade for the line with the wye is tied to the 4 mains, it HAS to start where the turnout was and the turnout needs to be on the same level as the 4 mains. Therefore, 2 grades are needed; one from the black dot to the blue dot and another from the blue dot to the cyan rectangle. As you can see, the grade from black to blue is 3.3% and the one from blue to cyan is 5.4%. That gets all the Level 3 track (green) under the Level 2 track (blue) so everything clears. But, with this scenario, the line with the wye will end up going down quicker that the 4 mains and will not be even after the turnout. My first attempt was trying to meet your goal of keeping them even until after they disappeared and there is no way to do that from the blue dot to the cyan rectangle with an acceptable slope. And the slope for the other line coming from the wye will be even steeper.
At any rate, I'm not saying this latest version won't work, but you're going to end up with grades above 5% and 6% unless the length of the grade can be increased. I don't believe those grades are viable for passenger trains, but I could be wrong. Most try to keep grades below 3% and some shoot for 2%. You can try to move the turnout further to the right and begin the grade further around the curves on the right, but there are still 2 more mains that need to be added/considered. When you add those, the cyan rectangle moves up and decreases the length for the grade. That's why I believe it's important to get the 4 mains set and BEFORE adding the lines with the wye (or turnout, whichever you decide to use).
I could be wrong here too, but it seems to me like you're having some difficulty understanding grades and where they have to begin/end. I wish RRT could display those better, but it can't, so I might still try SCARM. If nothing else, SCARM would display the colors of the tracks better. I've got other things to do though, so I'll let you mull this over for a bit. Look this over paying particular attention when I reference color points.
