Train pass vs Point-to-Point tickets and general advice

The European East Pass costs $211 for 5 days of travel in Hungary, Austria, Czech Rep, and Slovakia. That is cheaper than a Select Pass for the same countries and cheaper than full-fare 2nd-class tickets as far as the Swiss border (about $290). Seat reservations generally are not required, but may be for the departure from Budapest by RailJet (not other RailJet services).

However, if you're buying tickets for your fellow traveler each time, then the pass doesn't really add any convenience to your trip; you could buy two tickets as easily as one and might get a few with advance-purchase discounts if you're ready to lock in departure times in advance (see same link above).

Have you checked train schedules from Prague to Salzburg? With the above pass, you would want to travel via Linz (Austria), not via Munich (Germany). Toward Switzerland, the most direct route is a scenic and direct RailJet through Austria, so you're not likely to choose a German route. How to Look Up Train Schedules and Routes Online gives you the DB train schedule link and tips for using it.

Budapest to Vienna - 13 Euro
Vienna to Prague - 19 Euro
Prague to Salzburg - 19 Euro
Salzburg to Innsbruck - 9 Euro

That is 60 Euros. Not sure on the St. Galen leg, but not much. These are prices for tickets bought in advance, online for specific trains. As you can see, a rail pass is a luxury item where you essentially pay 3-4x normal prices for total flexibility. In your scenario, tickets just bought at the train station window on the day of travel would just about equal the cost of the pass. No need for a pass. Read this link for great info:

http://www.seat61.com/Railpass-and-Eurail-pass-guide.htm#Should%20you%20buy%20a%20railpass%20or%20pay-as-you-go

I normally price out point to points then compare it to a pass before my trip. I haven't purchased a pass since 2001. Part of the reason is I keep my travel legs short, so point to point is reasonably cheap. Once you get to longer travel legs, where a pass might be cheaper, you should probably opt for a plane.

The fare from Austrian Rail from Bregenz to St. Gallen is 15,40€/adult. Sounds like the Eastern Europe Select Pass would be preferable to a 4 county Select Pass including Switzerland.

Still, I would look at the individual, advance purchase tickets. I've always found them to beat a rail pass. They charge you an awful lot for lack of planning (also called "flexibility").

As far as Prague to Salzburg is concerned, the fastest route shown normally on the Bahn site is by regional to Linz and IC to Salzburg. That is about the only connection shown on the Bahn site without going through Germany and needing another country on your pass, but if you put in Linz as a stopover, it will show you more connections through the Czech Rep directly to Austria.

As for flying, the first to connections, Budapest to Vienna and Vienna to Prague are too short by train to make flying preferable. Salzburg to St. Gallen is just barely long enough by train to make flying preferable except St. Gallen airport has only charter flights - probably not economically preferable. Only the rail connection time from Prague to Salzburg is long enough to make slying a viable option, but there are no non-stop flights on that route. All flights require connections and the shortest ones are around three hours. That is just lift-off Prague to touch-down Salzburg and does't include time to/from airports, check-in, security, waiting to board, boarding, deplaning, and finding ground transportation. I'd say it would be faster by train. Plus, the fastest flight (2H55M) is by Lufthansa for $432.80 per person, one-way.