Elliott, I think you have come a long way on your plan! I'll let those with a better eye make suggestions, but I really like the little tweeks!
Yes, I agree you are close enough to plan benchwork. The two locomotives are definitely beauties!! They will look great running on your layout!!
As most have already stated avoid the pop ups. Around the wall is much better. I really like your final design. I had an N scale layout with pop ups and as my Dad would say"It seemed like a good idea at the time". It was a nightmare for me and as I aged became even worse on my back/knees.
I understand the need for a possible second entrance, but I really like the big sweeping double track curves on the peninsula. The reversing nature of these curves, even with generous radii, will make for some interesting challenges and visual effects with long trains.
My biggest feedback would be to add a reversing loop to add operational interest. You should be able to fit one in with minimal changes. ( see my red line)
Other than that, I get the desire to have as many trains one the table as possible, but the yard area seems very busy to me. Lots of parallel tracks without visual break ups and lots of switches that will be hard to reach. Not sure how to approach that but it seems that you will spend more time looking at the tops of cars than enjoying moving trains along that wall.