1st Trip abroad

Triberg is Cuckoo Clock Central, and I have the wood carving on the dining room wall to prove it. Easy to get to on the hourly regional train from Baden-Baden. Short bus ride from the train station up to the actual town.

Oh yeah, stop in to Papa Joes Biersalon in Cologne. Great collection of old music vending machines, and they're own contribution to the craft, Tuennes & Schael.
https://www.youtube.com/watch?v=PJhEVsKlHno
Weekends, live music, or at Papa Joes Jazz Lokal.

The Amsterdam portion of your trip is overly ambitious. Each of the museums is going to take at least a half a day to view the highlights. Both the Anne Frank House and the Van Gogh museum require that you buy your tickets in advance for a specific time slot. A walking tour of the Jordan District, the red light district etc will take a half a day each. If you take the Sprinter train from Haarlem to Amsterdam Central Station then catch the tram to the Rijksmuseum area, it is going to take you about an hour each way in travel time. I would recommend that you find a hotel in Amsterdam, if you want to make the most of it.

I suspect you're going to get pretty tired of moving to a new hotel every two nights once you leave the Amsterdam area. I don't know what to suggest to you, though, because you're hitting some rather small places that don't require long stays.

If the only thing you really want to see in Colgone (Köln) is the cathedral, why not hop off the train there, make use of the lockers, check out the cathedral, and then hop back on the train to Kamp-Bornhofen? It makes for a long travel day, but it eliminates a lodging change, and you can add the two nights for Köln to other stops on your itinerary.

I recommend the cathedral but if you want to see a bit of Prussian history, see the bridge, the figure on horseback is King William I, after 1871 Kaiser William I, the bridge is named the Hohenzollerner Brücke, Cologne is one of several cities in Germany where statues of William I stand

I agree with the idea of stopping over in Cologne for a few hours on your way to Burg Liebenstein/Kamp Bornhofen (or some other Rhine town.) There is luggage storage at Cologne station, and the cathedral is a few steps away from the station.

Day 9-11 - Rhine valley. Stay 2 nights in Bacharach. River cruise from Koblenz to Bacharach. Visit St. Goar, Boppard, Oberwesel, etc.

The cruise you are contemplating takes 4.5 hours and misses 50% of the most scenic part of the river (the part south of Bacharach.) Here's a map of the best part to cruise:

https://gruppentouristik.com/sites/default/files/anbieter%202/Bingen-R%C3%BCdesheimer%20F%C3%A4hr-%20und%20Schiffahrtsgesellschaft/Rheinlauf.jpg

Was your plan to use the cruise boat as transportation to Bacharach? If so, you will waste a lot of time getting to Koblenz and to the Koblenz cruise boat dock (and moving your bags with you as you go) and you will spend more time and money cruising a less attractive part of the river; a better use of time would be to take the cruise boat south from Kamp-Bornhofen to Bacharach (2hrs. 10 min.) Then you can drop your bags and finish your cruise (south of Bacharach) later that day (or on a subsequent day) so that you also see the more interesting Bacharach - Bingen segment (1.5 hours.) That's less than 4 hours on the river with a better scenic experience. One KD ticket from Kamp-Bornhofen to Bingen covers you for both segments.

Baden-Baden isn't the Black Forest. It's actually a place frequented for eons by Europe's wealthy elite and is mostly about spa treatments and casinos. B-B is also a very weak base town if you were to attempt day trips by public transport; the station is so far out of town that you need an additional round-trip bus ride just to use the trains.

Since you are going to Rothenburg anyway... why not condense your travel a bit? I suggest you allocate Day 5 to Cologne and your trip to the Rhine. Then... Allocate your saved Day 6 (which was Cologne) and Days 11-15 (which were B-B, Black Forest, and Rothenburg) to the "Rothenburg area." By staying in this region (known as Franconia) several days, you will cut down on your moves and you will have many great options...

Rothenburg ob der Tauber
Würzburg (Romantic Road town)
Bamberg (Outstanding place - beer Mecca - old town is a UNESCO World Heritage site.
Iphofen (old walled town of artists, wineries)
Nuremberg
SPA: Frankentherme in the spa town of Bad Windsheim (also home to a terrific open-air museum.)

You will not have time for everything in Franconia - pick and choose what pleases you - but you can still do a spa and see nice old-world towns (like those in the Black Forest.)

Almost forgot your cuckoo clocks... While you're on the Rhine, stop in at St. Goar (just north of Bacharach, (home of Rheinfels Castle) and visit the Cuckoo Clock Center (on the main drag, Heerstraße.)

You need to be aware that tickets to the Anne Frank House may only be available online and sell out quickly. I agree-stay in Amsterdam and do a day trip to Haarlem.

I was coming in here to tell you to cut Baden-Baden and the Black Forest, but Russ already did it for me. It's an outlier on your trip, and the least remarkable portion of it as well. The rest of it sounds great, don't forget to check out other towns along the Romantic Road in addition to the very touristy Rothenburg Ob Der Tauber. I really love Noerdlingen, for instance, and the recommendation of Bamberg is a great one! It's a beautiful city.

Thanks for all the advice. It gives me more options to think about.
This trip started out as a 1 week cruise on the Rhine and has morphed into 15 days traveling across 2 countries. And since I have never planned a trip like this I'm glad to see I'm not too far off track.