I've been looking at the April 19 travel schedule and it doesn't work well to do both the cruise and the trip to Rothenburg. Cruise on Apr. 18 instead. Here's a train itinerary for you...
Apr. 18
FROM: Amsterdam Bijlmer ArenA 9:02
TO: St. Goar 14:55
(Drop bags. KD Boat dock is in front of hotel. Buy ticket at dock and board 15:20 boat to Bingen (18:00.) Take train back to St. Goar after dinner (€7 each. However, you will each get a 20% cruise discount by showing your train ticket at the KD dock, which amounts to about €4 each.)
April 19
(See Rheinfels castle in the morning?)
St. Goar 12:00
Rothenburg 16:50
April 20
Rothenburg 13:09
Nuremberg 14:18
Right now you can do these 3 trips with one Saver Fare ticket at DB - €79.80 for two persons. How:
Search the DB itinerary page for a ticket on April 8 at 9 am from Amsterdam Bijlmer ArenA to Prague. Enter a stopover of 21 hours in St Goar and another for 20 hours in Rothenburg. Scheduling Prague as your final destination will trigger a stop in Nuremberg on April 20. You will not get on a bus or a train for Prague that day - you will forfeit that travel leg and end your trip in Nuremberg. (The reason for entering Prague is that the system allows for very long stopovers like the ones in this plan when you schedule a foreign destination.)
You then search for and buy a 2nd saver fare ticket for the direct IC bus from Nuremberg to Prague on April 21. Fares are showing at €15 - €20 each.
If you try to book the individual trips on separate tickets day by day, I think you will find it more expensive. Plus you'll have 2 more tickets to buy and carry around.