I don't have the book, so everything I'm saying is based on the little picture on the Atlas site.
I know it's an old plan, but I couldn't tell that by looking at it. From what I see, it's a single-track line with passing sidings, a few spurs, and a return loop. The question is, do you need that return loop? The only use I can think of for just one return loop on a continuous-run plan like this is to allow out-and-back running from that "yard". However, it's a bit of a small yard... guess that depends on how long your trains will be... but if you want both a freight yard and a repair facility, you may have space problems. Do you intend to do any out-and-back running? I can't tell what the minimum radius is. If it's 9.75", you should aim for bigger. I'm guessing you want a lot of 6-axle diesels like Dash 9's. At least 13" curves, then, preferably more. I'd plan for a couple more spurs, but I'd want to switch. With the mutiple passing tracks, it's good for running 2 trains at once, controlled by separate engineers. If you want to be able to let 2 trains run on their own, double track is preferable. I'm starting to realize all these alterations to suit (what I see as) your goals would make the layout much bigger. How big is the standard Longhaul Lines, anyway? And which crossover do you want to remove?