Are you aware of the fact that during the month of October many cable cars, gondolas and some cogwheel railways etc. will be closed because of the ending of the summer season?
By the time you are in Switzerland your choices concerning transportation in mountain areas will be restricted.
Travelling by train over great distances usually means that Passes which will give you free travelling (all the time or on days of your choice) are the most economical option.
A rough calculation of the costs of travelling between the cities you mention can be made with the Timetable Switzerland
and adds up to about CHF 350.
Please view the features of a Swiss Pass
. If you purchase Swiss Passes for two ore more persons travelling together you will get a 15% discount. This is called a Swiss Saver Pass (features can be found on the same page) and will be CHF 387 per person, 15 days, second class.
Whether this will be economical for you depends on other trips you are planning to make.
Another possibility: have a look at the Swiss (Saver) Flexi Pass
. The Swiss Saver Flexi Pass will cost between CHF 212 (3 days of free travelling) and CHF 337 (6 days of free travelling), also second class and per person. On the remaining days, a 50% discount applies on train, bus and boat tickets.
With these two Passes children up to and including 15years of age will be travelling for free.
If you have a Pass allowing you free travelling on the day you want to take the Glacier Express, you don't have to order a ticket for this train. (The Pass is your ticket).
However, you will have to pay for reservations for the Glacier Express, and reservations are obligatory!
Purchasing one of the passes can be done online on the mentioned pages, just click on "Order your … Pass here", then "Show more countries" and then "India".
Making reservations for the Glacier Express can be done through this page
. I am not sure whether you will be able to make reservations at this early stage, maybe this has to be done later, but try to do it as soon as it is possible.
For more questions I refer to the Railway FAQ
As for the weather: no one can tell you for sure. Be prepared for sunny weather with nice temperatures, for rain and for snow (!). In autumn everything is possible.
I hope I have helped you with these answers and I wish you a very pleasant stay in Switzerland!