
Chicago to Denver on the Zephyr, good choice. It's the most boring part of that train trip, but is worth it for the train riding experience alone. If you go sleeper, you get your meals chucked in as part of the fare. Coach seats are actually OK for one nights travel, they recline, are spacious, and the train is usually warm. You can get the same meals in the Diner as the 'First Class' passengers, just have to pay for them. You can slum it by getting snacks, and more importantly, a beer, from the Cafe downstairs in the Sightseeing Lounge Car (access to this car is available to all passengers).
We've done Denver-Omaha 3 times now, overnight, and went coach all 3 trips (2000 hrs to 0500hrs, hardly worth the extra fare for a bed, and too late/early for meals). Denver itself, has a good public transport network. There is a free shuttle service from near the station, up 16th. Each end of 16th are bus hubs to the outer reaches of Denver. You can catch a bus out to Golden, near the Colorado RR Museum, then a local, to the museum itself. We did, but check this out... can't seem to find the connection on the RTD website lately.
Can't offer any specifics on the other Colorado NG attractions, because I haven't done them. But, 4 of us as a family group (4 x Senior Citizens..... you can get SS rates from as low as 55 years of age) in a people mover (mainly for the luggage capacity) and used hotels. When we got to California, I saw a sign, Los Angeles, straight ahead, and Bakersfield (on the route to San Francisco) turn right... I turned right, took Highway 58, and 'found' Tehachapi and its famous Loop.
Of course, heading west from Durango etc you could divert slightly to the Grand Canyon, and maybe even Las Vegas, and a spot of the old historic Route 66. Just don't forget, the States is a bloody big place, and it takes a looong time to drive anywhere, even at 80 mph on the Interstates. Oh, and they drive on the wrong side of the road... no wonder there are so many accidents.
When you get to San Fran, dehire the vehicle as quickly as possible... parking is rare, and expensive. Use the MUNI, that's Cable Cars, Trolley Buses, Trams, and Buses. Catch the BART train to San Francisco International Airport, it drops you literally in the Departures Hall, as in, you actually have to go through the Departures Hall to exit the station.
This 'advice' is based on 3 trips to Midwest USA, and 11,000 miles of AMTRAK travel