5 Days in Germany this July

This is a bit too much in my opinion. 2 full days for Munich and Salzburg are quite rushed. What are you considering for your third city? If you really want to do the Rhine, then do that on day 4 and 5 because you'll spend half your day in transit there. Otherwise I'd stay focused on Munich/Salzburg/Bavaria and fly or take the train directly to Amsterdam from Munich.

I just did Salzburg in a day, it's possible. My other suggested city is Rothenburg. I just stopped by there for half a day and wish I was able to stay longer. and if you are driving that direction, I highly recommend it. Rhine Valley, you could do a short river tour and quick tour of one town and a castle in a day, but that will just be a quick overview, you won't get to see much and there's a lot to see on the Rhine River..but I have loved it so I suggest seeing something if you can.
I can't comment on Munich, haven't been, but I have been doing crazy one day tours of towns, with some it's very possible...it always feels rushed but when you really want to see certain things, you can make it happen...you just have to make sure you are up early enough to get on the road.

On your way to or from Salzburg, you could stop in Prien am Chiemsee (Chiemsee is a large lake) and take a boat tour to one or both of the islands. The island of Herrenchiemsee has a castle on it built in the style of Versailles. This area is located about halfway between Salzburg and Munich. The lake steamer landing is in Prien (one of them, the boat goes round the lake and stops other places, as well). The lakeside hotels have restaurants. Prien has a good website.

I am also going to be be in the area of Munich in late July so I have been looking at this a lot. Prolly going to go up to Rothenberg ob der Tauber for an overnight. For your Day 4 you might consider a day trip from Munich to the 2 castles outside of Fussen...Neuschwanstein (the 'fairytale' castle). Or if you are up for driving (I am not) a drive down the Romantic Road. Also, just outside of Munich is Dachau concentration camp/memorial. Or you could take a day trip south from Munich to the mountains. Take a quick look at a guide book like RS Germany or there is also one just on Munich and Bavaria.

You are traveling too many miles for just 5 days, I think. After Day 2 in Munich, I would head NORTH in the direction of Amsterdam, not further away from your destination. You could spend one afternoon/night in Rothenburg, then 2 nights in the Middle Rhine Valley - perhaps with a stop in Würzburg (where you must change trains) after Rothenburg. The Residenz (palace) there can be reached on foot from the train station in about 15 minutes. 2 nights on the Rhine is much better if you hope to visit a few villages, take a short river cruise, and tour a castle or two.