Mike, don't take this wrong, but I need to take a break, I feel like we're butting our heads against a wall. Every time I just about get all the disconnected track fixed and realigned, you post a new design idea and I have to start all over. I've already spent the better part of 3 days fixing various designs and now I have to start over again with the latest iteration, a design that doesn't come close to addressing the inherent problems and one that now exceeds the actual space (144").
For example, the O72's that you have "connecting" to the wye simply won't work, no matter how much of the other track you change.....and adding yet another version to the mix is DOA. In order to make that wye work, I believe you'd have to use an piece of O42 to get the correct angle and since your equipment requires O54, the wye will not work the way it is......no matter how nice it may look in SCARM. BTW, does your version of SCARM have the Snip Off tool or are you using an older version?
Then too, the 4" difference in the available space might not seem like much, but in your case, tracks are already close to each other and that's assuming they'll connect when things are cleaned up. You have a wiggly piece of flex track on both sides and I have no idea yet if they'll fit when that is straightened. I can guarantee things will not fit as is when the 4" is taken away.
The switch you added to join the white and yellow track adds no value at all to the layout, it duplicates the crossover further up and around to the right. And you don't really want a switch on a grade, especially since you're using trestles for your grades and not more robust support.
You've got the raised heights set to 5" in spite of all who said they should be 6"-6.5". I accepted it at the time because of the trestles and what track was going over other track, but now you talk about adding roadbed, mountains, etc. I'm not saying that can't work, but in order to make things work, we need to slow down and give those of us trying to help time to work on fixes before a new version gets posted. Or at least work on them yourself before you go off in a new direction.
Right now, the only section where height is a concern is the area above the double-crossover. Given that, you might be able to use a real hillside to raise the track on both sides and include them as part of the mountains. That said, the part above the double-crossover has to be supported by something that doesn't add anything between the rails below and the track above. I don't know if there will be enough room for that because something has to support the track above for a heavy train to pass over yet not be so big that it interferes with the crossovers below.
You're adding grades where you don't have all the track connected for SCARM to compute the slopes. It just happens that I think the grades for the yellow tracks are 3.7% and 3.4%. However, that doesn't take into account that the wye doesn't fit. Until that gets resolved, it doesn't matter if the grades are low enough or not.
You obviously haven't mastered the Snip Off tool because there are all kinds of track that need to be cut so things connect. I don't know if you've tried it or just figure it's not necessary at this point. Maybe I'm all wet, but you have a design you seem to like, so the goal now should be to see if you can get things to connect, not come up with something new.
And no matter how much you say otherwise, I still don't think you know what it's going to take to get this built, much less maintain it, deal with derailments, etc.. I don't know where you think you're going to stand or kneel after you add buildings, etc. I don't think you realize how small a 1' channel is when you're trying to do maintenance or reach over an incline to pick up a heavy engine that is almost 4' away, assuming you can wiggle up in the space to begin with. I don't even know how easy or hard it is to cut track and get them to connect properly, especially curves. Of course, I could be all wet and this will be a piece of cake. Maybe you see it as a challenge you're willing to accept and that's fine, but since I don't know your level of experience, I need to point out the pitfalls as best I can. Like I said earlier, if you think you can deal with them, I'm here to help with the design. I just don't want you to be blindsided after you've spent a lot of time and money on this.
At a minimum, I think you need to forget this latest version and continue working on the previous one, you can always take out the spurs if you need the space. At this point, the goal should be to get the major stuff working and then think about spurs, mountains, etc. You don't even have the white and black track working yet and you've added a wye and more grades. And no matter how "involved" the design looks in SCARM, the trains still run in ovals. It's great to have ideas, but adding more to something that doesn't work yet, doesn't help the process, at least not for me. As someone reminded me, designing and building a layout is not a sprint, it's a marathon.