A Saver Day Pass is a ticket that covers all public transit in Switzerland, so if you get that you do not to buy any other tickets.
If you however end up not buying a Saver Day Pass you will need a ticket Appenzell - Grindelwald via Chur - Disentis - Brig. Tickets in Switzerland are, like in most countries, for a route, not a train. You do not need individual tickets for each train You do need a seat reservation for the Glacier Express though.
Tickets are always available. You risk nothing by waiting.
But in your place I would get the Saver Day Pass.
The route you are planning to take does indeed involve a lot of transfers. But those transfers are short, and do not involve a lot of walking. You just walk from one door to another, dragging your luggage behind you. You will still do less distance than at the average international airport. But if you want less transfers just leave earlier. There are routes that only have one transfer.
And if you miss a connection you just take the next one. I know that is of no use if you miss the GE, but after the GE, from Brig onwards, you are just back to taking whatever is the next train to your destination, so the 5 minute change should not worry you to much.