Another misconception many Americans, Ozzies etc have of Europe - "see a capital and you've seen its country"
And yet those same people know better than to think that of their own capitals.
See what response you get if you tell an Aussie, "Oh yes, by spending 3 days in Canberra, I feel like I've truly visited Australia and experienced the culture."
On the one hand, I want to go to Salzburg for the beauty, the Alps, the Sound of Music, and because I feel it fits the "original idea" of the trip, which was Germany/Oktoberfest/Bavaria etc.
A logical solution would be to skip Berlin then. The city is very much worth a visit, but you'll have to come back to Europe anyway ;-)
By skipping Berlin you can also add some more Sound of Music experience to the trip by going into the mountains. You can go for a hike, take the cable car to the peak of a mountain, visit some cute little Austrian villages etc. Relatively close to Salzburg you can find the highest mountain in Austria (Grossglockner), the National Park Hohe Tauern, the salt mines, lakes, fortresses etc. See http://www.salzburgerland.com/en/ausflugsziele/index.html for some more inspiration.
You can easily spend a week in any of those cities. So your itinerary (I am referring to your original one) is doable and gives you a bit of time to see the main sights. It does however not allow for any recreation and no time for catching the spirit of those cities (and this is quite different between Prussia, Bavaria, Bohemia and Austria).
Skipping Prague would not spare travel time since the trains Berin-Vienna do pass Prague anyway. Going Berlin-Salzburg-Vienna-Munich by train means travelling Berlin-Munich-Salzburg-Vienna-Salszburg-Munich. This makes the orinial routing more senseful. And Berlin-Prague between Dresden (dont get off the train - another week) and Prague along the Elbe and Moldava rivers is an fine scenery. Esp. the Elbe valley between Dresden/Pirna and Usti nad Labem is a highlight, only matched by the middle Rhine valley.
As for train tickets and reservations, these do not come together in Germany. Im not 100 % sure, but also not in Austria and the Czech Republic. In Germany you can buy a ticket without reserving a seat and you can reserve a seat without buying a ticket. There are two types of tickets: Standard fare, which are fully flexible and good on any train going that direction, and reduced fare, which are only valid on a specific train+date. This leaves you the option to buy reduced tickets for trains which you are sure you can take (and reserve a seat additionally or leave it) or to buy standard tickets if not sure. For example you can reserve seats on three different trains out of Frankfurt to Berlin (fee is 4 Euro pP for one reservation) and. jump on any of those. This wastes a bit of money, but gives you reserved seats for sure. If in a hurry, you can even buy the tickets on the train for a small surcharge (cash or credit card).
Some ideas for the driving bit: From Munich along Walchensee, Fernpass, Füssen (Neuschwanstein), Lindenberg, Lake Konstanz, Ravensburg, Mainau, Stein am Rhein, Schaffhausen.
Edited by: AnhaltER1960