Advice on Scenic Swiss Rail Routes (off season)

Looks like you are going to be there for about 2 weeks. The Glacier Express does start up on December 10, but all of the rail routes will be running as normal, at least one train per hour in each direction.
Standard advice is to skip Zurich and go straight to Luzern from the airport. Then to Interlaken (part of the Golden Pass scenic route), then to Montreux (rest of the Golden Pass scenic route), then to Chamonix, to Brig and Disentis/Muster (part of the Glacier Express route). You could turn around there and go back to Andermatt, then to Goeshenen, Erstfeld, and Luzern (part of the old William Tell Express route minus the boat ride).
Trace out your route with this map of the Swiss rail lines.
https://www.sbb.ch/content/dam/sbb/de/pdf/freizeit-ferien/ferien-kurztrips-schweiz/internationale-gaeste/uebersichtskarte_synoptic_map_2017_low.pdf

"The scenic trains are not running while I'm there" What you mean is that the trains with names and specially branded cars designed to suck large amounts of surcharges from gullible tourists may not be running.

Do you mean can you go part way along the Glacier Express route and then divert to Luzern? Yes, from Brig only go as far as Andermatt. Change for the short but impressive ride down to Goeschenen (sit on right). Then you are back on mainline trains and go go to Luzern. Doing this would miss the climb over the Oberalppass to Disentis, which is spectacular when not in cloud.

Steve,
YES!! That is exactly what I need!! --- so on to Chur from Chamonix (hopefully not in the cloud), you cracked me up with what you said. :) Switzerland is already taking every penny I have, so I am extra appreciative of your advice.

Sam,
I have to go to Zurich because a friend is going out of their way to meet me there for a day. So, from Zurich you think it's worth it to skip Bern and Murten and proceed to the route you suggested from Zurich? So, Zurich, Luzern, Interlaken, Montreux (maybe up to Lausanne?), Chamonix, Chur, Appenzell, (and surrounding area) Stein am Rhine. Your route looks pretty solid and if you think it's worth it to skip Bern I trust that you know.

You guys -- I'm thinking the ride from Chamonix to Chur looks too long for one day. Any advice on how to break that up?

You guys are the best -- honestly your help is super important to me.

Also, Sam that map rocks. Thank you for that. I printed it and taking it with me.

//probably ignore this part because I don't want to confuse the issue...any further, but --- if it helps...from Stein am Rhein I'm heading over to Colmar & Strasbourg (via Basel) to take advantage of my Swiss pass as much as possible. Thanks again.

diverting at Andermatt is only half way to Chur.

Going all the way to Chur and then all they way over to Luzern would take too long.

That is why Disentis/Muster is a good spot to turn around. If you divert at Andermatt, you miss the Oberalp Pass, which is perhaps the most scenic part of the route. Disentis/Muster is the point where the the operating railway company switches from the Matterhorn Gotthard Bahn to the Rhaetische Bahn. The actual Glacier Express always stops there for 30 minutes for crew change.

As you will be traveling on a Swiss Travel Pass, you can change plans on the fly. Say its an overcast day, and the Oberalp Pass is in the clouds. Then you can just decide to get off in Andermatt and take the train to Luzern via Goeschennen. If it is clear, stay on to Disentis/Muster and go back to Andermatt and experience the pass in the other direction. All depends on you and the weather and how long you want to sit on a train.

Hi Sam,
Okay. I understand. I think I'm good now. Thanks for taking all the time to help. Happy travels. ;)

And when you are in Disentis, stop an hour there and visit the baroque abbey, ten minutes walking from the station. You may have lunch at Stiva Grischuna (three minutes from the station), but I warn that Graubunden delicatessen are some of the heaviest food conceived by human mind.

Great advice! Much appreciated. It gives me something to look forward to after such a long train ride. :)