Help with itinerary /train tickets for October trip to Germany

You could use a Bayern Ticket to get to Neuschwanstein departing at 9;41 am and getting you to the ticket office by 12:20 pm. Make a reservation for 1 pm. including the return, cost is 39 EUR total for 2 people. Train to Fuessen then bus to the castle ticket office.

You could make an early morning train to Vienna with a scheduled stopover in Salzburg for the day before continuing on to Vienna.
Then train to Prague, then train to Berlin. Deutsche Bahn will sell the ticket to Salzburg and Vienna. You can use OEBB for Vienna to Prague and DB for Prague to Berlin, or use www.cd.cz for a better price for these 2 trains.

I hope you get sightseeing suggestions as well as your inclusion of Austria- I did use the train (flew into Munich) to get to Salzburg to meet the RS Tour. I had purchased the train ticket upon arrival to the Munich main station from the airport, felt so organized and- still don't know what happened:
This was early June, and a lot of construction in and around the station The departure day I eventually- it was a mess- found the posted sign for the Salzburg track - once on board, the conductor eventually came through after about an hour and said I was on the wrong train! ??? I just absolutely panicked! The train even said Salzburg on the front!
He then asked if I had 20 euro, which I gave him. ?!
And he moved on, and the other passengers assured me it was going to Salzburg. So I believe there was more than one train option for Munich-Salzburg at about the time on my ticket, and likely mine was for the cheaper one, and I had boarded at the wrong track?
Regardless, it stopped several stations before Salzburg (construction?) and then we were all shuttled onto another train to complete the journey, adding about 1/2 hour to the arrival time.
My fluent French and zero German made reading signage a challenge. Just a caveat, if you are counting 100% on train travel. I always thought trains in Germany were supposed to be really reliable- there's a couple recent posts about challenging experiences, too.
This is not at all meant to discourage your transportation plans, and I love trains, but just to be sure you plan for understand the system and options better than I did! What a wonderful trip!

If you do decide to do Salzburg as a stopover, you can by a ticket now for 100 EUR for 2. Take the 7:23 RJ train and specify a 6 hour stopover in Salzburg. you will arrive at 9 am and have until 3 pm to get the RJ train to Vienna, arriving at 5:32 pm. There are later trains as well, like 8:16 or 9:29.

Thanks for the responses. I'll look into the suggested trains.

My current plan has us in Salisbury for 2 days - then Vienna for 2-3 days- then to Prague for 3 days before heading Berlin.

Should I eliminate the days in Salzburg? Got more time in Vienna and Prague? Thanks.

In Prague I use the Boutique Hotel Domaine Balthazar, which is near the end of the bridge in the new town.

thank you. Looks great...