Robert, my son Andy is also autistic and he still talks about his ride on the C&TS many years ago (he is in his mid 30's now). He has ridden both the C&TS and D&S, not to mention many miles on the wider gauge railroads. And in general he loves riding the train. All the noises and motions fascinate him. But as you note, all the activity may exhaust him so a break in-between is probably wise. And as you know autism differs person to person, so your mileage may vary. But hopefully both of you will have a great time.
With regard to where to ride, my only comment would be on the D&S it is kind of a devils choice. The open cars provide great views, but on a cool wet day can be miserably cold. The regular coaches are cramped, the seats small, and you can't see much, but they are protected from the unpredictable weather. If the weather looks nice, you can't beat the Silver Vista with its comfortable ex-airline first class seats. But my favorite car is the Alamosa with its rear platform. As others have noted, on the C&TS everyone has access to the open gon, and the coaches are roomier, so the choice of accommodation is less critical....it's all nice.
Have a great trip.
JBWX