All right, I've had time to sleep on this one.
I don't see a German 2nd cl Youth Twin Flex Pass, only individual passes. A 3-day is 157 EUR, so for 2 that would be 314 EUR. This is still more than the cost of an Adult German 2nd cl 3-day Twin Flex Pass for 292 EUR. So that is the way to go.
You have 6 travel days total. I've already gone over the cost of combination local verkehrsverbund tickets (8/15,8/19, Berlin-Wittenberg), QdL ticket (8/18), and Sparpreis tickets, (8/20,8/27). 599.10 EUR with restrictions as to time of travel, advance purchase train specific,
Alternative to get 2 German 2nd cl 3-day Twin Flex Passes for 584 EUR (2 times 292) plus the local tickets on the other 3 days for 71.90 EUR bringing the total to 655.90 EUR.
The 4-day, and 5-day passes seem to be in a sweet spot, at 314 EUR and 335 EUR. So if you got 5-day passes, the cost would be 670 EUR plus 19.10 EUR for the trip on 8/19 bringing the total to 689.10 EUR. This would bring in several advantages.
On the day of your arrival, you would be using a pass day, so you would get the 20% KD discount. Secondly, if your flight was delayed, or you had a big delay getting through immigration (it happens, job actions, whatever) and you could not make the 16:30 KD boat at Bingen, you could still continue on to Boppard that day on the train and be covered.
On the day trip to Wittenberg, you could take an earlier fast train and not be restricted to traveling after 9 am or only local trains to and from.
The trip from Rothenburg to Nuremberg will always be best with the VGN Tagesticket Plus. There is no advantage as to time (its a Saturday), number of connections, or travel time. There is a connection every hour to Nuremberg and it takes from 1 1/4 to 1 1/2 hours to get there. That is a local verkehrsverbund ticket, the Greater Nuremberg Transit Authority (VGN). 19.10 EUR covers all of you for the day and includes local transit (buses, trams, U-bahns) in Nuremberg.
For the long distance trips, especially Nuremberg to Berlin, you might also want to spring for seat reservations at 4.50 EUR each to guarantee you can all sit together. It is a Sunday and appears to be busy because the Sparpreis tickets are already expensive or nonexistent on certain trains. Among other things, the Bayreuth Festival is going on at that time.
Hopes this helps.