Germany Vacation

Koblenz and Cologne are close to one another so perhaps you could just stay in Koblenz and avoid having to unpack again. I don't know about your leave constraints but days 8-9 is really only one day, and same with 10-11. There is a lot to explore within the Rhine corridor so if you were to add days anywhere, I would give an extra day here.

The first day in Munich will be consumed by jetlag and settling into the new environment, so that only leaves one day there, not enough to add Dachau, and particularly so if you want to see Munich well (for instance you could spend about 3 days in the Deutsches Museum alone).

I would probably think about cutting something from this itinerary. You can do an itinerary like this if you are on a tour, because tour operators have all their ducks lined up in a row and just shoot, but it's much harder when it's just you, and maybe a you that doesn't yet know how the train system works, etc. You will also have to figure out what your priorities are. At the moment you have either alpine Germany / Austria, or Rhine with little villages and cool Cologne. If you can't do more than 12 days I would drop one of these areas depending on your priorities. I assume you are looking at an open jaw ticket. Is anything set in stone yet?

Lavandula

Overall, you might be better served adding one night at your stops and removing one or two destinations or treating them as day trips. Possibly add a location between GP and Koblenz. Also, you didn't say where you're flying out from.

1-3: Munich w/ day trip to Salzburg
4-6: GP w/ day trip to Fussen
7-8: Nuremburg/Wurzburg? Some midpoint in between Alps and Rhine.
9-11: Koblenz w/ day trip to Cologne

You mention "scenic drives" but also mention train times as if you're travelling by train. Train and drive times can vary greatly in Germany, especially when travelling between the Rhine and Alps. When I visited a couple years ago, we drove from the Rhine to Rothenburg ObT then to Fussen. Driving saved a lot of time. Perhaps rent a car when leaving Munich then return the car in Koblenz?

First, why are you flying into Frankfurt the first day and spending 3½ hours on the train getting to Munich? Why not just fly into Munich?

I think I've heard this before. You are using FF miles and they only fly to Frankfurt. But you're losing most of the first day to use your miles.

Maybe you can organize is differently. Take a train from Frankfurt to Cologne, then work you way back via the Rhein Gorge to Garmish-Partenkirchen, then Salzburg and fly home from Munich.

The other problem, as I see it is that you are spending too many days travelling. A travelling day is mostly wasted - packing up, checking out, getting to the station, travelling, getting from the station to you next accommodation, checking in, unpacking. Try to minimize travel days.

You have 12 tour days, which is 11 real days. You're spending five of the travelling, that's only 6 full days at a location.

But, hey. That's basically my way of travel. It's your trip.

Agree with others that you should really look to cut something from this trip. 12 days is not a lot of time, and rushing around a reasonably sized country will get tiresome. Also, Deutsche Bahn is famed for its delays, which will almost certainly impact you and cut even more time from your itinerary.

We are interested in seeing fairytale castles, Alpine scenery,
medieval villages, wine country and scenic drives at a relaxed pace.

You've received some good feedback here about pacing and the number of places. What about the atmosphere you are looking for? Right now, the big-city base towns feel at odds with your goals. Of course you want to stay where you have a good choice of hotels and restaurants, but variety is certainly possible in places much smaller and much more more "old-world" than Cologne and Munich (1 million plus each!) These cities don't sound like what you have in mind. Salzburg, which does have some atmosphere, has around 160,000 residents and is no village. Even Koblenz has 100,000+ inhabitants (and not all that much atmosphere, btw; like most German cities, it took a beating in WW II and was never quite the same after reconstruction.) Generally speaking, places that are closer in size to G-P would likely suit you better.

I notice that nixit71 has suggested Nuremberg as a stopover town. Good point, and a place you'd probably like. Nuremberg is a big-city exception; the reconstruction there was done thoughtfully, and the old-town center has retained much of its old-world charm.

I'll get back to you with some adjustments/suggestions.