The best thing to do about finding out best prices is to look for special offers like "Sparpreis"/Promo/Superpromo etc., mainly all the Railway companies in Europe got couple tariff stages - first they sell those promo tickets for less, afterward go for more expensive ones until it reaches regular tariff fare.
You can easily search for cheapest offers on the selected route really simply - try picking any dates from one to three month in advance and take a look at best offers at that date, then take a look at the other day etc. In such case after checking couple different dates you will exactly know the best offer available
Rothenburg, Dachau and Fussen all in Bavaria, so Bavaria ticket works for all those places - no need to worry here.
Golden pass route is pretty good, so go for it. Concerning tickets - you just need to mention your exact route while purchasing ticket (if it will be international ticket Innsbruck or Fussen-Zurich-Luzern-Interlaken etc.). If you will try purchasing discounted tickets like Europe-Spezial from Germany to Switzerland or Supersaver tickets for domestic Swiss travel just make sure you "connect" tickets to your timetable in order to avoid long stopovers and delays.