Once again, this is why I love the participants on this forum!
Dovecote, I would have also expected (logically, imo) that AGR would be the one to offer the compensation, not Amtrak CR. I will certainly remember these posts if it happens to me. Thanks, amamba and Alan, for clarifying this very important point.
I don't know that this is too much to handle for one trip (though I wouldn't personally attempt it). The best thing to do is break up your trip.
For example, travel from ATL to WAS and then on to CHI and then on to EMY. There's plenty of time to connect between the Crescent and the Capitol Limited, and the Cap is generally pretty good about getting into Chicago on time.
Then, instead of trying to connect to the northbound Coast Starlight on the same morning, spend a night in San Francisco. San Francisco is a beautiful city, and there's lots to do. Make sure to book a refundable hotel room, so that if the Zephyr is late, you can cancel that and catch the Starlight. Having one night in the Bay Area gives you a buffer in case something happens.
Then take the Starlight up to Portland or Seattle and spend another night before catching the Builder. I think the Starlight to Builder connection is a little tight, but probably doable.
And then take the Builder to Chicago and spend another night. The Builder to Capitol or Cardinal is probably one of the worst connections to try and make.
Staying overnight in San Francisco and Chicago would extend your trip by 2 days. It would, however, require you to shell out a few additional points:
>35,000 points ATL - WAS - CHI - EMY
>20,000 points EMY - PDX - CHI
>20,000 points CHI - WAS - ATL
Total - 75,000 points
Compared to:
>35,000 points ATL - WAS - CHI - EMY
>35,000 points EMY - PDX - CHI - WAS - ATL
Total - 70,000 points
Note than EMY/San Francisco is a natural break point. AGR is going to make you split your itinerary somewhere on the West Coast because "circle" trips are verboten. And it's a crapshoot whether they'll route you on the Zephyr when the Builder would be a direct trip for CHI-PDX.
Since you have to break your trip on the West Coast anyway, why not break it at Emeryville and spend a day or two in fabulous Frisco?
If you don't want to break your eastbound trip in Chicago, you could always break it in Milwaukee or even Minneapolis. From Minneapolis, they'll bus you to connect to the trains in Chicago if the Builder is running late. From Milwaukee, there is frequent service on the Hiawatha into Chicago.
A couple of the PM's I've received agree with your first sentence about the scope of the trip length! I think a less ambitious trip might be prudent, but I'm having trouble coming up with an itinerary that shortens it very much. My priorities are the CZ and the EB, so the middle of the trip can't change much. Changes to the beginning and end don't seem to save much time off the total trip length. Any "insurance" changes tend to get lengthy and more expensive. I realize this is still a bargain trip, $$ wise, though, even with a couple of hotels.
Yes, almost everyone seems to agree that the CHI EB to Cardinal or CL connection is very hit or miss. That's why I was considering the CONO, although that adds an overnight, too--but not an additional AGR award for the overnight, and it cuts out one zone.
There are two reasons I haven't considered breaking the trip in SF:
a) The CZ to nb CS is apparently one of the safer connections of the whole trip, esp if EMY was changed to SAC if need be. Although anything can happen, the connection from the CS to the EB in PDX is much, much tighter. It remains to be seen what AGR will let me do within a zone, however.* Results are varying greatly according to recent posts.
b) I've seen a little of SF, it is a beautiful city, but honestly, I'm still very much missing my late husband, and exploring cities by myself just doesn't sound like much fun to me right now. Someday, maybe. That's just a personal thing. I would enjoy being on the trains, however.
*If I decide to fly into DEN, I'm hoping I could do a 1-zone (western) award DEN-Wolf Point (but not an overnight in WPT), and then another award from there. There is no other route within the western zone to get from DEN to WPT, so I think they would allow it in a separate 1-zone award.
Please elaborate on the advantages of Milwaukee or Minneapolis, especially as to how they would make the CHI connection safer. I had not considered those.
Thanks, everyone! All of this is so very helpful.