Switzerland itinerary Help - two to three weeks by train in Sept / Oct

Seems like you've thought through the train adventures. When you have an option, spend 2 or 3 nights, not one. You will need a day off the train now-and-then. And in a mountain location like Zermatt, 3 nights is better as the weather is fickle. Staying 3 nights gives you two full days so a better chance of seeing the mountain. This is true in any mountain location.

If you can go for three weeks, do! Spread the fun out and stay a few places for more than 2 nights.

As to lodging, start with Rick Steves' Switzerland guide and check Booking.com or other booking sites.

Thanks Laurel for sharing your thoughts.

Sounds like a fairly good plan, with just a few holes to fill in.
Here is a rail map of Switzerland which shows where your pass is valid. You should get a copy of this with your pass: https://www.sbb.ch/content/dam/infrastruktur/trafimage/karten/karte-sts-pass-gueltigkeit.pdf
Note all the rail routes shown on this map (in red) have at least one train an hour.
You can look up train times on the SBB website: https://www.sbb.ch/en

Next use Bernina Express to Tirana and then get to Lake Maggiore or Lake Como, which one and how? Thinking 2 to 3 days

You DO NOT need to use the Bernina Express. There are other trains (once per hour) on this route.
You can get an Italian train from Tirano down the east side of lake Como heading for Milan (not covered by your pass because it is an Italian train). But you are then on the wrong side of the lake to get back to Switzerland. If you look on the map you can see a yellow Swiss bus route which runs from Tirano to Lugano. This only runs once per day.
You can either stay in Lugano (or somewhere else on that lake), or north from Lugano then west to Locarno on Lago Maggiore.

On to Zermatt, taking Gotthard Panorama Express from? to Andermatt, to meet with Glacier Express going west to Zermatt. Doable?

Again, forget about the named trains. There is one train per hour on all routes. The tunnel (both old and new tunnels) go UNDER Andermatt, north-south trains cannot stop there.
Option 1: from Locarno, west to Domodossola (scenic Centovalli line), then on to Brig, Visp and Zermatt.
Option 2: North to Göschenen (north end of old Gotthard tunnel), double back south to Andermatt, then west on Glacier Express ROUTE to Brig, Visp and Zermatt.
Option 3. North to Airolo (south end of old Gotthard tunnel), bus over the Gotthard Pass to Andermatt (yellow on map), then west on Glacier Express ROUTE to Brig, Visp and Zermatt. The bus only runs a few times a day, and stops in October because after that the pass can be closed by snow. So this option may not be possible.

Take Golden Pass train to Interlaken for 2 or 3 nights

Instead of Interlaken, stay somewhere further into the mountains south of Interlaken.

Next up to Lucerne, via Gotthard Express? for 2 or 3 nights

What is this with the named trains? This is not even the Gotthard Express route. Just get one of the hourly trains from Interlaken to Luzern (local spelling).

Back to Zurich for 1 or 2 night(s) before leaving the next day.

Skip Zürich. You can get from Luzern to Zürich airport in 70 minutes. Use the time for the other places you have listed.

Finally ENJOY!

Thanks Chris for the very helpful info and guidance.
This is the kind of info I was hoping to get. I was using the named train routes from the Rick Steves map, thus the reason for all the named trains, which I have learned are not needed.
Instead of Interlaken it looks like Murren or Gimmelwel.
Very helpful info on Lake Maggiore / Lake Como area and Andermatt, thanks.