Welcome, Sgreenphoto! The CZ is an amazing trip, and I really hope it works out well for you. I've taken the full trip a number of times, and when I lived in San Francisco I had the luxury of taking a short overnight trip up to Reno and back the next day.
It's a shame that Amtrak is so confused these days that you can't count on getting a room, or when the train will leave (or arrive) or if there will be a Sightseer Lounge, which is IMHO an essential part of the experience. But we only hear about the times they have problems, so presumably most trips are still completely successful.
If for some reason a car is cut from the train, causing a downgrade, there is an order in which cars are cut, and there are people here that can tell you which car is the safest. I don't have it in front of me but hopefully someone will come along and post that info. It would help if you post your car number. If you are in the highest risk car, you can call customer service and try to change to a safer car.
I'm glad you were able to get a bedroom, they are very nice.
Anyway, post any questions you have here, and we'll try to answer them.
p.s. My avatar photo was taken off the web, but I am old enough that I took the original California Zephyr the last year it was run before Amtrak took over. If you want a Vista Dome now, you're going to have to take the Canadian some time, highly recommended!