Which town to shorten stay?

Stuttgart.

How long do you have in the "middle Rhineland area" you mentioned? That's between A'dam and Stuttgart, but you don't have the number nights on your list.

"4 nights for GaPA, Salzburg and Munich"

4 nights for all three of those places?

Munich is very underwhelming in my opinion. 1-2 days is enough. Unless you plan to take a trip to Dachau Concentration Camp -- if you need day trip tours from Munich (Dachau, Regensberg) I highly recommend bighattours.com - he is amazing.

Our trip:
USA to Amsterdam (arriving Sunday)
3 days Amsterdam (bike tour, day tour-Zaanse scans, edam, Volendam etc, Anne Frank house, Van Gogh museum, attend Mass)
--ICE train to Frankfurt (pick up rental car head to Middle Rhine Valley)
2 nights Oberwesel staying in Hotel Schoenburg castle (boat cruise Bacharach to Boppard, biking the Rhine, drink reisling, travel to burg Eltz)
2 nights Stuttgart ( visit Heidelberg, porsche museum and trek somewhat into the Black Forest)
2 night Rothenburg (night watchman tour, walk the wall, crime & punishment museum, side trips to little towns)
4 nights around Munich area (breakdown below)
----1 night in Munich for Dachau & Schleibheim Airfield Museum
-----1 night at GaPa for Neuschwanstein Castle, visit Zugspitze peak, Partnachklamm & hopefully St. Peter & Paul Church
-----1 night Salzburg for Salt mines, SOM, Mozart birthplace carry over into most of next day
-----1 night Munich for flying out the next day (might try to sneak a museum in if get back in time from Salzburg)

We have 13 days and fly out on day 14 (Saturday). Think I need more time in GaPa area or Salzburg?

IMHO you are right - you do have way too much on your plate for the "Munich area." You actually should be looking at 5 nights to squeeze all that in.

• I would in fact Leave Rothenburg by noon on "R'burg Day 2" , see a "little town" or two ON THE WAY to Dachau (your next destination) that afternoon, and spend the night in the pleasant town of DACHAU. There's no great reason for driving into Munich just to sleep there one night. This way you gain an early start on Dachau and the airfield museum without making a long journey that morning first morning from Rothenburg.

• "2 nights Stuttgart": (You can save a night here for GaPa, where your time is crazy-short.) Driving from Oberwesel, you should have time to stop in Heidelberg for a few hours on the way south (if you wish, not a "must" IMO) and perhaps to see the Porsche Museum that afternoon. However, a better stop for you than Heidelberg that morning might just be RHEINFELS Castle (only 5 minutes from Oberwesel, good for kids.) Again, if you have no goals in Stuttgart proper, I'd spend one night near the Porsche Museum (north of Stuttgart) and avoid the city. Zuffenhausen has hotel options for you right there. When you wake up there the next morning, I'd skip the detour to the Black Forest. Head instead toward Rothenburg for this night. The area you'll pass through makes for good scenery.

• Rhine cruise: There are no direct boats from Bacharach to Boppard this year except the 17:15 - 18:50 boat. Also, doing this cruise segment forfeits 50% of the most scenic part of the river (see this map.) The wise move is to cruise the whole scenic part from Bingen to St. Goar (which also gives you 1.5 boat hours.) Boats for St. Goar leave Bingen at 9:15, 11:15, 14:30, and 16:30. You just need to get to Bingen (by car or by train) first, then return post-cruise from St. Goar to Bingen (if you drive there) or from St. Goar to Oberwesel (by train.) It's actually best to view the river for the first time from the boat, so rather than driving your rental car from FRA along the river to Oberwesel, could you drive from FRA airport straight to Bingen? Park there, cruise north to St. Goar; train back as outlined above.

• The weird letter in Schleißheim is not the letter B, but a symbol for the sound "s". You can write "ss" instead of "ß"

Oh wow! Thanks Russ and everyone for the insight! First time to Germany and traveling with kids! Thank you for your input!

You are packing a lot of stuff into this trip, and I think you are going to have to cut a few things along the way. I guess you can make those cuts on the fly.

First, you are going to need a big car, a van possibly, to fit 5 people and all the luggage. where were planning to rent the car, Frankfurt Hbf or Frankfurt airport? You should be able to find the size you want at the airport, at Hbf I don't know. There is a direct ICE from Amsterdam Centraal to Frankfurt airport at 7:38 getting there at 11:49. Figure about 1 hour to get the car and get everybody loaded, so leaving the airport at 13:00.

Now I don't know how you feel about leaving a car parked at Bingen KD dock with all your luggage for several hours. Germany is a very safe country, but I would worry. I will let others advise on that. Alternative is to drive to your hotel in Oberwesel, check in and drop your luggage in the room. That would take you to 15:00. You could then drive to St Goar and take the 16:00 KD boat going up river. That is the slow way, but then it is very scenic cruise, the slower, the better. That would get you to Bingen at 18:50 and you can get a train from there back to St Goar to get to the car and drive back to the hotel. There is a train from Bingen Stadt at 19:31 you should make no problem that gets to St Goar at 20:00.

There is plenty to eat on the boat, from snacks to full dinners.

--ICE train to Frankfurt (pick up rental car head to Middle Rhine Valley)

One additional thought to simplify the logistics on this day, and to get you to Schoenburg earlier...

You say you have 3 days in Amsterdam. What if, instead of spending your final night in A'dam, you retrieved your bags from your hotel's front-desk after your sightseeing, then took the DIRECT late-afternoon ICE train (maybe the 16:38?) to Cologne (19:13) and slept there? Then you pick up your car in the morning and drive straight to Oberwesel or to Bingen for the cruise.

Cut one night in Rothenburg and one in Stuttgart and add to GaPa. There is so much to do in that area, and it is truly beautiful. Rothenburg is cute, but incredibly over touristy. You can see it all in a day. In Garmisch, the Zugspritz is spectacular, and you can stop off at Lake Eibsee. Also check out Partnach Gorge. Day trips to O'Gau, Mittenwald, Ettal, etc. are easy. Your kids will enjoy the adventure side of Garmisch. The train ride back to Munich for a night is quick and easy for your return flight home.

Is the Porsche museum the only reason you're visiting the Stuttgart area? Because it's fine if you're a big fan of rare Porsches but very underwhelming in other regards. The Mercedes museum is a lot better and you don't mention that...leading me to think you could skip Stuttgart entirely. I say this as someone who thinks Stuttgart has a lot to offer but you're really short-changing other places.