Advice on 30 day Itinerary

What you essentially have here is two distinctly different trips. The order that you have the trip is not exactly the most efficient. I would suggest you get some good maps or go on Google Maps to plot your trip.
It's a shame you've already purchased the tickets, because this is an itinerary that would have been best to fly open jaw into one city in the north and out of one city in the far south.
Note: I've stayed in Bacharach and Koblenz a few times. I find it a great one night stop, but it's not a real destination since the city's just about 1/2 mile long or less. You also might be trying to take on too many cities.

Agree a lot with David. The other thing we do on our extended trips like this is to plan a dead day every four or five days. Gives an opportunity to catch up on laundry if necessary, maybe sleep in a bit adjust for the busy days, and, most importantly, to deal with the unexpected. Something new that want to see but had not planned to see or maybe something was closed and we want to circle back. Anyway we have slack in the schedule to handle changes.

It is likely to be extremely expensive to rent a car in Croatia and drop it off in Slovenia. Check on that right away, because depending on public transportation for a travel leg may substantially increase your time in transit and perhaps the number of nights needed at one or more destinations.

Positioning a seaside town between Mostar and Plitvice will add to your travel time.

Make Fussen (castles?) a daytrip from Munich during your initial stay. There is a direct train from Bled to Munich (it starts in Ljubljana and stops at the Bled station before proceeding north).

That is one less stop, but you really need to eliminate one or two more or you will feel too rushed.

Janice,
Since you don't want to be rushed and have already hinted you need to eliminate some of the cities, I would suggest you cut the westward potion of your plans (Rothenburg ob der Tauber, Bacharach, FrankFurt, and Cologne). Then make a loop from Munich to Dubrovnik and back. This seems more logical geographically, to me. You could add Salzburg if the cut hurts your feelings.
I hope you have a great trip!

We did the RS Adriatic tour a couple years back. We flew to Munich and spent a couple days there, then Salzburg for a couple days (train), then a beautiful train ride to Ljubljana. If on our own, a car would be helpful in Croatia as trains could be sparse as you go south. Slovenia was better but still not like in Germany.

Flying to or from Dubrovnik, car in Croatia (and side trip to Bosnia), then train (or reverse this). Would work. Or, after Plitvitce, drive to Zagreb, then fly out. Renting a car in Slovenia and returning it in Croatia, or vice verse does add extra cost, but with 2 couples the time saved would be worth it.
We also found trains in southern Germany were convenient and relatively inexpensive except getting to Rothenburg which was a little more complicated—we went there from Bacharach, then on to Munich and it involved trains and a short bus ride at the time.
Agree with above posters. Have a down day every 5-7 days for laundry and relaxing. It’s a vacation not a race.
Enjoy your trip!

Thank you all for the advice. Patty, the insight you added was very helpful. Would you remove Rothenburg de ober from the itinerary? We would prefer not to rent a car in Germany and use trains/buses as needed. We understand crossing borders with a rental car can be a bit expensive, but will follow through on that.

We are still going west in Germany towards the Rhine and Mosel Rivers, then find the best place to fly from, to Croatia. We are thinking Frankfurt as we found a great price from there to Dubrovnik, then car, train the balance of the trip as needed.
Thank you all again. It is very helpful!
Janice

It sounds like you are committed to the western Germany plan. A few thoughts...

St Goar and St Goarshausen, right across from each other on the Rhine and connected by a ferry, will have their annual wine festivals beginning Thursday 19 September (or maybe Wednesday -- schedule is not up yet) and culminating with a big fireworks show over the Rhine (Rhein in Flammen) on Saturday 21 September. This can be watched from the banks of the river or from ships on the river.

If you are going to Frankfurt only to catch a plane, here are 2 other options that are near Cologne:
1. Eurowings has a direct flight from Cologne/Bonn Airport to Dubrovnik on Thursdays and Sundays. Flights for late September right now are priced from 59 euro for the "bare bones" fare and 87 euro to check a bag weighing more than 8 kg; prices tend to go up as tickets are sold. The airport is a 15 minute S ride south from the the main Cologne train station
2. Eurowings has a direct flight from Düsseldorf airport to Dubrovnik on Tuesdays and Sundays. Flights for late September right now are priced from 69/96 euro. The airport is a 45-50 minute train ride north from the main Cologne train station

If you want to visit both the Moselle and Rhine valleys from a single location, Boppard may be a better location than Bacharach because it is significantly closer to Koblenz, where the two rivers come together.

Thank you so much. Great information!