Being retired for 23 years, we haven't traveled in high season for decades, but even when we did, we never made advanced hotel reservations and I think that even today it is not as necessary as most people seem to think. Just to check, I searched Kayak for rooms in Rothenburg for two days from now, July 7, 2019, and got a choice of 9 hotels. The great advantage of not booking ahead (and travel by car) is infinite flexibility in where you go and what you see and when you do it.
Alps: The Swiss Alps are no better but more expensive than the French or Austrian Alps. When we did travel ins high season, we found that room prices were bargains at ski resorts, and so is the scenery (again: travel by car). Example: a three bedroom corner suite with balconies on two sides facing the Alps, Big Screen TV with a library of Hollywood movies, breakfast and dinner and a bottle of wine for two people, all for $120 (current prices).
We have done about 18 vacations in the Austrian Alps by car (straight shift). I would never credit the Swiss Alps with better scenery than the Austrian Alps. Oddly, the most attractive Swiss Chalets are found in Austria's Tyrol region.
You probably have too many days allocated for Fussen, and when you are done there, head into Austria to the Oetztal where you will find what maybe a perfect honeymoon hotel, Hotel Bergidylle Falknerhof This pension well worth seeking out. To find it, start up the Oetztal road toward Solden. Turn off the main road on the road to the upper Stubing Falls. Keep going up hill past the falls for several miles to the little village of Niederthai. Turn right just beyond the little chapel on the right side of the road. The hotel is located in the group of buildings a bit further up hill.
Niederthai is a little ski resort set in a pleasant mountain meadow that must have a population of at least 9 people-- a perfect pastorale get away from it all setting.
I've done a bunch of posts on seeing the Austrian Alps, most aimed at trying to get people out for Salzburg and Hallstatt, so I'm not going to repeat. You can find them under my posting name.
Besides being cheaper, the Austrian Alps beat Swiss Alps for bad weather options. When we drive in the Alps, we plan two itineraries, one for good weather-- the mountains-- and one for bad weather, towns and museums. The most scenic areas of the Austrian Alps are around Salzburg and Innsbruck. Nothing in Switzerland can compare for good/bad weather and scenic options.
I rented a Hertz car at Munich airport. After I got home, Hertz charged my Amex card $1,100 for unspecified "damage" to the car. I complained to Amex who asked Hertz for proof of the damage, and that was the end of it. Amex canceled the charge and I don't rent from Hertz now.
Since you lived in NY, you have seen the Black Forest. In NY,. its called the Catskills, Adirondacks, and Appalachians. But unlike the low mountains (Catskills, Adirondacks, and Appalachians; Black Forest, Jura, and Vosges) the high mountains are all different. You allready know that the Alps are not the Sierra. Skip the Black Forest, or just take a cut across. and go into France to the Route de Vin Alsace, the superstar of quaint EU villages.
And while you are an your way to Alsace via the Black Forest, go along the north shore of Lake Constance with a ferry boat ride to Mainau Island and visits to the Baroque churches off the NW end of the lake.
Must preparations for driving in EU:
Both of you must memorize the International road signs.
Get the Michelin Green Guide for every country you will be in-- incomparable for planning and none better for getting you around once you get there.
Get a good paper road map, 1:200,000 is best. 1:500,000 is minimal. I prefer Michelin.
Goggle everything you can find on driving in the countries you will be in, especially the official national web sites.