Germany Route

Not sure what anybody else will suggest, but I'd get to Koblenz and then follow the Rhine to Frankfurt, then Wurzburg, then Nuremberg, to Munich, to Salzburg. Very easy by train, all 1-2 hour trips if you just go straight thru. 3-4 weeks if you go slow.

Flown into Frankfurt a few times but never visited. As KGC suggests, Wurzburg, Nuremberg and Munich will easily take up your 4 days, although you will miss out on smaller towns and villages along the way.

"...best route, scenic towns to see/stay on the way?"

With 4 days I think it would be wise to plant yourselves in one place - like Nuremberg - and take an excursion or two from there to some smaller, scenic towns.

Nuremberg is no "town" but it does feel like a smaller place within the old town zone.
https://munique-tours.de/private-tour-guide-munich-bavaria/Nuremberg-from-Albrecht-Duerer-House.jpg
https://tourismus.nuernberg.de/en/discover/places-of-interest/hidden-places/

From Nuremberg you can hop on a train to Iphofen (adorable old walled town in between Nuremberg and Würzburg, direct train, 45 minutes.)
https://tourismus.nuernberg.de/en/discover/places-of-interest/hidden-places/

Another great outing from Nuremberg is the Franconian Freilandmuseum in Bad Windsheim. It's about 1 hour away by train.

https://www.tripadvisor.com/Attraction_Review-g198421-d284746-Reviews-Frankonian_Open_Air_Museum-Bad_Windsheim_Middle_Franconia_Franconia_Bavaria.html

A local train day pass for two adults called the Tagesticket Plus costs about €20 for two and covers the round trip journey to both places.

https://vgn.de/en/tickets/all-day-ticket-plus/

Würzburg: This is a nice city to visit as well. If you want to visit it, I suggest you stop there on the way to Nuremberg and visit for several hours. It's right on the way. Leave the Rhine/Mosel area early, get off in Würzburg and stow bags in a station locker, then see the towns.

We lived in Germany for 3 years. I suggest that you travel by boat from Cologne to Mainz. Beautiful church in both cities and the Gutenberg Museum (printing press) in Mainz.

Cologne > Mainz by boat is only possible if you book a multi-day, European cruise vacation.

Day cruise boats cover much smaller segments. KD Cruises will show you the most scenic part of the Rhine between Bingen and St. Goar in 1.5 hours. 5 boats per day cover this segment in a typical season. This year there's just one daily boat (14:00 - 15:40.)

Schedule: https://www.k-d.com/fileadmin/schiffstouren/KD_Fahrplan_ab_Juli_2020.pdf

While in the west, don't miss Rudesheim and Trier.

Also, Heidelberg.

On your way to Salzburg, take the Romantic Road.https://www.romanticroadgermany.com

Munich is a must do.

Folks, please; they have 4 days. How anyone could do Rudesheim, Trier, Heidelberg, Munich, and the Romantic Road in that time boggles the mind. Likewise boat trips; they're great, but even one day on a boat and they're running out of time.

Month of the year? With four days, I'd suggest focusing on the most scenic part of the Rhine, the Middle Rhine beween Bingen and Boppard. Since the train is far faster than the boat you'll use for that northward ride, you can see any other towns that make your list without difficulty. You aren't explicit about wanting to see remnants of very old towns, or if you want to see the superb museums of rebuilt Cologne and Frankfurt. We decided not to spend time on slower boat rides of the Mosel, and focused on wineries (appointments required) and Trier by car. Do you have Rick's "Germany"?

We used a rental car, but it is quite reasonable to do this by train. I'm not sure I would go as far as Salzburg, because there is so much to see in Germany. And there are several major airports all around Germany, for two-segment flights home. (Are you currently flying home from Vienna or Munich?)

** Between Rhine to Salzburg we will have 4 days to spend.**

Is this 4days/3nights then? If so then I'm with Russ and pick one spot between Rhine/Salzburg for those three nights. He listed several good options. Personally I would spend them in Frankfurt or Munich but that is just me.

If you have 4 nights then another option would be 2 nights in 2 locations. Here you could split between a large city (Frankfurt or Munich) and smaller ones (Nürnberg, Würtzburg, etc)

DJ