The idea of substituting a shore excursion for a visit to an FKK is simply the best thing you could ever do! FKKs are the most wonderful places on earth (I think Disney has copy written "Happiest Place on Earth??). The only thing I am concerned about is the amount of time you have. I find that I enjoy rolling in early afternoon and I don't end up leaving until after midnight! I am there to soak up the ambiance, enjoy a couple ladies and just generally have a good time. I don't speak a lick of German, but I get by. At times I have used Spanish, or French but those are rare occasions, English is just fine.
The other threads are very accurate. While I have visited FRA many many times, I don't ever go to the big-name FKKs as I find them impersonal and full of "sharks". I have been to many in Bavaria, but my hands down favorite is FKK Feigenblatt in Worms. This place, is unlike the large places that charge 50-60 Euro entry and feature a nice buffet. It has a 15 E entry, no buffet and is a small cozy place. I have never had a bad experience and the girls are in no rush to separate you from your euros. I have found that to be the case in the larger busier places as the girls bounce from guy to guy trying to tantalize them with their wares. Worms is right on the river and it claims to be one of the oldest towns in GErmany next to Trier. I suspect your tour may stop there.
Of course, I have tried larger scale places on occasion. Colusseum (?) in Augsberg is nice, and when I am not out in the Rhineland to enjoy Feigenblatt, I tend to head to FKK Hawaii in Ingolstadt (home of Audi). This place has the 50 E entry and buffet, but is very relaxed and has a small FKK feel. However, I don't think Ingolstadt is on one of the rivers you mention.
Regensburg is a University town. I have never been to any FKKs but have had wonderful reports.
I hope you have a great time, I wish I could be your tour guide...drop me a line if you have any questions and I'd be happy to provide more info if I have it!