Munich to Amsterdam - where to go in between?

All of those are good choices and I think three nights is a decent amount of time to spend in each of those. With regards to Salzburg, it's so lovely there that a little backtracking isn't going to matter. It's not that far from Munich and is worth a little bit of effort to get there (and it's not that much effort, believe me). In fact you can use the DB Bayern Pass to get to Salzburg from Munich which would lessen your cost considerably.

That said, if it were me I'd probably drop Strasbourg, which is a lovely city but I don't think you really need three nights there. Instead head up to the Rhine Valley, which you said you were interested in. I was there in 2022 and spent three nights in Boppard, which is relatively easy to reach by train. I stayed at the Bellevue Hotel (Bellevue Rheinhotel). It was a very nice hotel that sat right on the water (practically). You could walk out the entrance and walk straight down to the KD cruise line about a hundred feet away, along with all the other attractions along the the water. They gave excellent service and many of the rooms have balconies overlooking the Rhine.

And Boppard is a good town to base in. It's small enough so that you're not overwhelmed by people, but large enough to have a good selection of restaurants, cafes and hotels. Plus you can take the train up to Bingen then pick up the KD ferry and ferry back upstream towards Boppard to see all the beautiful castle ruins along both sides of the river. It's really lovely. I would also recommend a visit to Burg Eltz, which is a gorgeous castle in a breathtaking location. Another castle worth visiting is Marksburg.

Well it looks like you've added some cities, ha ha!

I still would think about eliminating Strasbourg unless you have some really compelling reason for going there. Although you could to leave off the Rhine area and instead base yourself in the Black Forest. If you did that and stayed in the absolutely beautiful town of Gengenbach (which I promote heavily because I love it so much), you could still get to Strasbourg from Gengenbach on a day trip, as it's only about 40 minutes away by train. And if you stay in Gengenbach, you will enjoy the wonders of this beautiful town with its lovely cafes and restaurants and gorgeous half-timbered houses. It's really beautiful and I loved my stay here.

Another advantage to staying in Gengenbach is you would be entitled to receive the KONUS Pass which entitles you to free public transportation throughout the Black Forest, including train rides. There are some lovely things to see there including the gorgeous open-air museum and several other small towns that are off the Black Forest Railroad and are incredibly charming. You could also make your way to Tubingen for the day as well. The nice thing about Gengenbach is that it's relatively undiscovered by Americans and so you will mostly find other German travelers there. I highly recommend a visit here.

I was looking at rhine valley but not sure which area to stay in and it looked like some places were harder to get to by train and in that case where could we skip on our list? Any recommendations would be greatly appreciated!

You are probably using a weak information source. There is almost nowhere in Germany worth visiting that is not accessible by train.

The German Railways site (DB) shows departures at 7:28, 9:28, 11:28, 12:45, and 13:28 from Munich to Boppard. The journey takes approximately 5 hours and requires one change of train, either in Fankfurt or at FRA airport, depending on the departure time. Later departures from Munich are also possible.

In between those departures are other journeys which require 2 or more changes of train (less desirable.)

For a very different look at Germany than you will get in Munich, I enthusiastically support mardee's suggestion for Boppard as a base for a few days for the reasons provided and for many others. Marksburg Castle in the fine old-world town of Braubach is not to be missed if you wish to tour a castle with a true medieval feel - and it's only a stone's throw from Boppard:

https://www.loreleyvalley.com/images/map/rhine-map440.gif

Boppard information:
https://www.boppard-tourismus.de/media/was-ist-wo-broschu__re_en_190219.pdf

You'll have free rail and bus transport from Boppard to other nearby places if you stay there, thanks to the VRM Guest Card:

https://www.boppard-tourismus.de/en/accommodation/

Other destinations on the scenic left-bank Rhine railway which you can visit from your Boppard base:

St Goar / Rheinfels Castle ruins (see Rick's materials, 10 train minutes from Boppard
Bacharach (see Rick's materials, 20 train minutes from Boppard)
Remagen / WW II Peace Museum (50 train minutes from Boppard)

Or take a train ride up the pretty Mosel River as well. The Rhine and Mosel railways are known as the most scenic train routes in Germany.

Cochem (1 hour from Boppard, on the Mosel River; combines nicely with a visit to Burg Eltz in a single day.)

Traveler, what do you look for? Why did you choose these cities which are partly a significant detour?
History, architecture, food, ...? More concreteness would help to do recommendations.

For help the link to the actual long-distance train network:
https://cms.static-bahn.de/wmedia/redaktion/aushaenge/streckenkarte/Liniennetz-ICE-IC-2026-Stand-09-2025.pdf

Most of the places you listed except for the Rhine Valley and Heidelberg are out of the way.

You could easily stop in Cologne and see the famous cathedral. You could continue down the Rhine that has many great sites to see, or head straight for Munich. Consider Wurzburg and then taking The Romantic Road down to Augsburg, then turn left to Munich.

Many great small medieval towns to see like Rothenburg ob der Tauber as well as Augsburg.
https://www.romanticroadgermany.com