This will probably be my last update to this thread. I've taken many things into consideration and I wanted to share one of the last drastic trackplan updates I've made. I'll probably do some tweaks here or there, but for the most part I think I've settled on this basic overall idea.
The dark green level is 10" off the board, which puts me at a grade I'm comfortable with. It also allows plenty of room underneath for scenics, or additional track. The red line is my downward slope, and the light green is the up. Since I removed the reverse wye in the southeast corner, I'll tweak that and use it for train parking, or another siding for industries. I'll probably add a spur here or there once I see a real-life rough version for some more train parking or industry sidings. I was originally thinking that I'd keep the second level from coming down to the first, and that would allow me to separate my conventional and controlled locos a little more logically, but since I think I have a good compromise. Everything should be reachable as well.