Everyone gets an answer here, sometimes it takes a little time.
As for your questions: I don't have all the answers, but I'll try my best.
Day 1 - Looks fine.
Day 2 - Visiting the Chocolate Factory in Zürich, then leave for Interlaken and visit Thun and Spiez seems a lot to me for one day, especially if you want to visit the Beatus caves as well. If I were you I would skip one or two of your plans. I don't know how much time you want to spend in the Chocolate Factory, but it will take you about two hours to reach Interlaken.
Day 3 - If you want to reach Jungfraujoch and Trümmelbach falls from Interlaken, you can't use the Golden Pass Line. Kleine Scheidegg isn't a city (just a railway station, hotelc etc., but with beautiful views!, Wengen and Lauterbrunnen are rather small but nice to see. So, it depends on your time schedule whether you can take the time to look around there. Starting the day rather early would make things easier.
Day 4 - Looks fine and is all doable.
Day 5 - Bern and Basel in one day can be done too, but also here I wonder how much time you want to spend in those cities. Travelling times can be found on the Swiss Timetable
. If you really want to explore both cities, it might be a bit much.
Days 6, 7, 8 and 9 - Journeys with the Glacier Express or Golden Pass Line are absolutely beautiful. And because you consider visiting Geneva and Montreux, the the Golden Pass line would be my first option. Again, visiting the Cheese Factory and the Chocolate Factory in Montreux: it can be done, but it depends on the time you want to spend there, the same goes for visiting Geneva and Montreux on one day.
Yes, there's a lot more interesting to see :-). If you browse a little, starting from the home page of this website, you will find lots of hiking tips and day trips.
I hope this helps and I wish you a very nice trip!