We wanted to do the Glacier Express but it is not running in November
The Glacier Express is an extra train for tourists. The regular trains on that route run hourly (all rail routes in Switzerland run hourly or better). And you see the same mountains out of the window, whichever train you take.
You say "7-9 days", that's 6-8 nights. A good rule is never less than 2 nights in a place, 3 is better. That makes 3 different places. You will have to cut back your plans - sorry.
"not opposed to taking train connections on our own but we will be traveling with luggage." - luggage is not a problem, except you are responsible for all luggage on trains. You are the only person who carries it, and puts it in the racks on the train. You need to judge how much you can carry.
Third point, November is between seasons in the Alps. Summer hiking season is over, but too early for skiing. Some* hotels and restaurants will be closed, but many will be open. Weather will be variable with snow at high levels.
And where do you want to fly back from?
All that said, this is my recommendation.
1) From Venice, train to Varenna on Lake Como
2) From Varenna take a train as follows: Tirano - Bernina Express route (OVER the Alps) - St Moritz - Chur (1 night). I chose Varenna as it is on the route from Milan to Tirano, no doubling back. Continue by train to Luzern, 2-3 nights.
3) Next, somewhere in Germany. What interests you?
Possibly: Train to Zürich airport (70 minutes), fly to Berlin, rest of the time in Berlin.
What do you want to see?
