Welcome to My Swiss Alps.
<<"We also need our second home base. I was thinking of staying in Zurich on October 4th since we are departing early on the 5th for this last night only. So any thoughts of where to make our second home base??">>
For a good base within easy train ride distance to Zürich Flughafen, Luzern comes to mind.
I hate to pack and unpack and waste time by staying at too many places. You are wise to limit your number of bases. That said, you probably could be comfortable with three bases instead of two for a 14 day trip.
I am puzzled by your long list. (Yes, I know, so are you. ;-) )
As far as I can tell from your note, you want to "see" these places. I also see the verb "do." But, I don't know what "do" means. I don't know why you want to go to those particular places.
The other verb that we get here a lot is "cover." Thanks for not using it. ;-) I don't know what that means, either.
I do know what "see" means. You can see most places in 5 minutes. Get off the train. walk out of the station, and look around, go back in and get on the next train. So, perhaps you want to do more than "see." Maybe you want to explore? It takes time to explore the old city of Luzern, for example. And, you probably have some criteria for "what to see" and, more important, "what to do." Can you articulate them....possibly with some reasons "I like old cities" "I like to walk in mountain scenery."
Why do you want to see the Swiss National Park?
Maybe you can select ideas such as -
take easy walks, or,
take moderately difficult hikes, or ride a lake boat,
or ride special scenic trains,
or, visit historic churches,
or, visit art museums,
or, eat at vegetarian restaurants,
or, explore the little know but excellent wine scene that has developed in the last few years.
Force your self to rank those things, in an ordered list. Let the top items on the list help guide your choices..
Some places are better than others for those items, so, if you can rank the reasons or "to do's" m, you can helps us refine your choices.
If you want to see "High Alpine Regions" make a list of the ones in your list. There are several. Aggregate the ones in the Jungfrau region ( near Wengen) in a single group. Assign a fixed number of days to those. Since - by your criteria so far as we understand them so far - they are all good, it doesn't matter which ones you throw away. Go there, and sort them out after you arrive.
List all the other high Alpine regions and throw away most of them. Unless, those are the only things that you want to see. Still throw away most of them, but keep a few.
Go to the Jungfrau region first. Late September is still great. As you get into October, the chances of weather issues in the mountains increases.
Have you been to Niagara Falls? If so, skip the Rhine Falls. If not, skip the Rhine Falls anyway, and go to Niagara.
Put some of the others on a map.
I use thumbtacks or sticky notes on a large map when I plan a trip to a new country. Do that, then throw away the geographic outliers, unless they meet some of your selected criteria.
There are good resources to help understand how long it will take to get to these places:
map.search.ch/?pos=637384,161088&z=32 &poi=bergbahn,halteste lle,zug
map.wanderland.ch/?lang=en&route=all&bgLa yer=pk&resolution=20&X =636060&Y=157880&layer s=Wanderland
By the way, you forgot the Engadine...whether near St. Moritz, or, my favorite at the end near Austria - Scuol, Ftan, Guarda and Ardez. Just wanted to make sure that you had enough to choose from. ;-)