Which itinerary?

The two itineraries are not comparable. You can go fast or slow with both, and you can find typical German food and good beer in both, but beyond that...

A) is strongly rural, great if you're into nature/scenery, small towns with old-world character, castles, outdoor activities.

B) is strongly urban, better if you want museums + churches, city walks, city trappings, shopping, etc.

Which sounds more like you?

If it will be A), you might wish to arrange to visit Oberwesel (a few towns south of Boppard) on April 30, when "Wine Witch NIght" takes place... There's a parade and other formalities that evening when locals gather to ring in the new wine season. A new wine "witch", traditionally the daughter of one of the area's vintners, will be selected and crowned as this year's royal spokesperson, fireworks will light the sky, and the previous year's witch (a straw witch, actually) will be burned on the town's main square as a farewell to the previous growing season. A pretty unique festival, I think.

https://oberwesel.de/wp-content/themes/yootheme/cache/56/Weinhex-25-6-scaled-560a24c6.jpeg

Cologne: I like the „Brauerei zur Malzmuehle“.

Boppard: please have an eye to there could be a lot of constructions for the big garden show 2029, next year, I think.

You aren't including Berchtesgden and Salzburg as well as Garmisch/Fussen.
Of course, it depends on how much time you have.
Cologne's cathedral is worth a visit, but with you short time, consider skipping.

Both ideas sound good to me, was hoping for some helpful insight to sway one way vs other and move ahead in planning. What I really need is 3 months a year and an unlimited budget

What I really need is 3 months a year and an unlimited budget.

Ha ha ha, I know that feeling! Seriously, though, Russ is giving you good advice. Think about what you really like. Would you rather be in cities or in small towns?

Both of your itineraries look fine. I've been to all of those places you named and I enjoy them all, but I have to say that I would probably vote for "A" if it were me. I love Cologne and I love the cathedral, and if you do go there, I would highly recommend a day trip to Aachen (which is a quick 30-minute trip by train), as it is a charming town, has a beautiful cathedral, and also houses the remains of Charlemagne. Gengenbach is one of my favorite places in Germany, and I would go there in a heartbeat. I love the Black Forest as well. I also stayed in Boppard, and it's just a gem on the water.

But I also enjoyed my time in Berlin, Munich, Rothenberg, Bamberg, and so on. So think to yourself what you really want to do. You also might think about going to YouTube and looking at some videos there. Do searches for the various towns and cities that you've listed, and take a look at them and see which one pulls at your heart a little bit. I've done that before, and it usually works very well.

Having said all that, I suppose there is an option C. You could combine a few. For example, I don't know where you're flying into, but if you're flying into Frankfurt, you could start off in the Rhine (logistically I think that makes more sense), skip Cologne, then head east to Rothenburg and Nuremberg, and then down to Munich. Basically, 3 to 4 days in the Rhine, 3 to 4 days in the Nuremberg area, and then a couple of days in Munich.

Both good choices. Having a preference for smaller towns and a bit of scenery, I'd choose option A. I'd also substitute Cochem for Boppard (I prefer the Mosel), and drop Cologne.

With A you could also check out the Alsace area of France for something a little different. When I was based in Strasbourg for a f days for Christmas markets I did a day trip to Gengenbach, a great little town. If you choose A you might also want to check out Freiburg as well.

Will this be your first trip to Germany ?