Germany and Austria - HELP

You should be aware that May 25 is a public holiday in Austria.

"take the night train at discounted fares...." There is no night train Munich to Vienna, I take night trains, have two planned for the trip in a few weeks, but there is no need to do that here. Munich to Vienna is a bit over 4 hours. The night train goes Munich to Budapest. If you change trains in Salzburg, take the Westbahn to Vienna.

I have just one suggested alteration to your plan. On May 25, you show going from Salzburg to Rothenburg and return to Munich. It will take 5 hours to get to Rothenburg on the train, so noon would be your earliest arrival giving you just 5 or 6 hours in Rothenburg before returning to Munich to spend the night, then get up and take a train to Frankfurt. Rothenburg is about half way between Munich and Frankfurt. Stay in Rothenburg overnight and then take the train to Frankfurt the next morning. As was pointed out, May 25 will be a holiday in Germany and Rothenburg will be very crowded during the day, but much quieter in the evening and you can take the famous Nightwatchman Tour. I hope Herr Baumgartner is still doing it as he has a dry sense of humor and a practiced delivery. http://www.nightwatchman.de/index.php?active=Home&lang=en

I have looked over your itinerary, and, sad to say, you should have come here first and saved the money for the GRP. I looked it over, and even if you turned in the pass unused for a 15% penalty, you would still save money, but only about 30 EUR. There is something to be said for the convenience of the pass, so I would not bother doing that and stick with what you have. Use it for May 13, 14, 16, 17, 18, 25, 26. For the trip to Europa Park Rust, use a Baden-Wuerttemberg Ticket that includes the bus from Ringsheim station to Europa Park. Leave at 9:30 am and get there by 10:45 am and you can return whenever you like. The cost is 28 EUR for the two of you, leave after 9:00 am. You buy it from a ticket machine or pay 2 EUR from the ticket window. I also understand there is Kombi-Ticket available in Deutsche Bahn Vending machines that includes round trip train and bus on regional trains from anywhere in Baden-Wuerrtemberg plus park admission.

Berchtesgaden may be best answered by others more familiar, but it looks like you could get a 12-zone ticket for 11.50 EUR per person to cover the buses from Salzburg to Berchtesgaden and most of the popular areas and back to Salzburg. The website is in German only, but you can use google translate.
http://www.rvo-bus.de/oberbayernbus/view/tarif/wabentarif/wabentarif-ueb.shtml