Thank you both for the helpful replies.
The ballasting of a whole car yard at once seems a little overwhelming to get it perfect for me. Don't get me wrong here, I'm happy that I am moving forward. I agree that some better detailing might be the ticket so thanks for that idea. That should help the look of the finished product.
I think it's extra frustrating because of the volume of tracks right there right now. I thought ballasting would be slightly easier and I just threw it down to get it done with. Maybe the practice will help with all the rest of the mains. At the least, it has taught me to slow down here.
I am also upset that I didn't use cork to raise the tracks. I feel that it makes it tougher to get the ballast deep enough and yet add some interest like ditches along the tracks. That will come when I do the mains though.
The switches seem to be a tough spot to get the ballast vs. operation correct. I would go shallow there but again, I'm forced to make it level looking with the rest of the yard. So I keep picking at it while it dries. The glue is all over everything and although I wiped it down, there seems to be a haze of dried glue that I still had to scrape off the rails. The rock size I first chose seemed to big so I blended crushed in with it afterwards. Then more glue and more cleaning!
