The file doesn't include any track heights, so I did some playing around. I lowered the yard 7" and that yielded 3.9% (lower left) and 4.8% (upper right) grades. I then lower it 12" and that yielded grades of 6.7% and 8.2% respectively. IMHO and based on the size of the yard, etc., all those grades are too steep for the size of the trains I assume are envisioned.
Obviously, the track leading out of the yard on the right is unfinished. I assume the idea is to join it to the upper lines near where the unfinished tracks are coming out of the curve. However, there is also an unfinished track jutting out to the lower left of the bridge. I see where that might also be a place where the tracks could join, but there is no way for that track to go under the curve out of the bridge and above the yard unless the yard is lowered at least 12" plus the thickness of the roadbeds. Even then, I'm not sure the grades would be acceptable.
I further played with connecting the yard and the new grade is 3.3%, but I don't know if it clears the yard and I didn't try to deal with the 8.8% grade on the other end. I also fixed a couple of broken joints and got the simulation to run through the entire layout, but I have to say is was kind of hard keeping track of all the turnouts with all the tracks active. It was easier when I hid layer 2.
FWIW, here's a photo and I included the RR-Track file.
