Just a couple of comments on the SCARM plan. There are multiple places where the track does not line up, mostly look due to a mismatch in lengths - so expect to trim some track. One section about at the bottom right has an elevation change when it should be flat - not a big deal because it will be obvious when you lay down the track. I suspect there are also mismatches at curves, but if you have some Gargraves flex track - an easy adjustment. I found it helpful to run the basic train simulator mainly to check for disconnects - kind of fun to watch the layout in operation prior to build.
I would pay attention to the near 4% grade on the rising sections. This will limit the train car length to avoid slipping. Be careful about the transitions between the 4% grade and flat. You have limited space to make smooth transitions. But since you cannot run the larger engines, it may not be a problem. (I found a couple of places where my Premier MTH 4449 rocks a bit (track is not perfectly flat in those areas) and will derail from time to time. The smaller RailKings run with no problem. I cannot help much on the yards and staging - I just know not having enough is not fun, and changing the layout later is even less fun - unless its a destroy and start over fresh.)