<<"We have decided to base in Lucerne, Wengen or Grindelwald and Fribourg for easier access to various sites. St Gallen is actually one of the "go to" places on my wish list.">>
Well, as Rockoyster illustrates, you are not really far from anywhere if you are based in the middle of Switzerland.
However, my suggestion was simple.
You have a strong interest in older towns...architecture, ambience...if I read your preferences correctly.
Based on that, I simply suggest that you go to St. Gallen instead of Schaffhausen. If you go there from Luzern, it adds about a half an hour to the journey, vs. Schaffhausen.If you want to you can make a loop with St. Gallen and the Rhine Falls, but If anything, and in spite of the tourist density, Stein am Rhein would substitute on my priorities for der Rheinfall.
For me, partly because we stayed in St. Gall on our first trip, there is certain emotional appeal. We came into town on a train from Liestal, and it was the last day of the Federation Jodlerfest. There were a bunch of people wandering around the old town in traditional clothing (or costumes, if you will). Some with with alphorns, and one guy was playing his alphorn on the sidewalk just outside the station. Those memories stick.
I work hard to go back to have a meal at Weinstube zum Baümli, near the Abbey. It has been there a long time. The building is over 500 years old. One floor up from street level. Wonderful ambience and good Swiss food.
I was not suggesting that you skip the Berner Oberland. That is by far the best known and most impressive tourist attraction in Switzerland, in my opinion and that of many others.
If you really want to see Schaffhausen, you could add it to your hypothetical next trip. ;-)
However, we each have our own opinions and interests
Regarding the rest of your trip, I share your interest in Fribourg. I have visited there many times, from Zürich, from Ligerz, from Geneva. Stayed there a couple of times.
It is a good base to do the things you have listed. When I am near there, I usually stay at Ligerz at the Kreuz, because I have become friends with the innkeeper and his wife. Simple, comfortable. Excellent cook, nice rooms.
Or, Hotel de l'Ours, in Sugiez ( that commune is now consolidated into Bas Vully) , for bit of luxury. The innkeepers are really nice people.
I used to do overnights in Murten/Morat when i worked in Geneva, and would suggest it as a place to consider for a visit. The old town walls are intact, and you can walk on them.
I have a couple of favorites in Fribourg.
The first is a restaurant.
In Fribourg, the restaurant au Sauvage ( a.k.a, der Wilder Mann), in the old town ( which nominally still speaks German) is probably the best in Fribourg. They have rooms, which are very nice, but not particularly cheap. They are a bit farther from the train station than you might like, but if you are not in a rush, there is a bus or you can walk 5 minutes to the funicular and then another 5+ to the train station.
The second is an interesting walk. The Gotteron Schlucht.
We have walked out to the end at Ameismühle, , turned right to go up the hill a bit and then right again across the meadows to le Bourgillon, then down the hill to the main square in the old town.
This one shows the route:
www.wandersite.ch/Tage swanderung/806_Fribour g.html
And,an initial comment about your days near the Jungfrau:
As proposed, day 7 will be the least "Swiss" of your days there.
Interlaken is a good place for rail connections to the rest of Switzerland, and Harder Kulm is fun. But, the city itself is more a place to sleep than a place to explore. That is why we always recommend the villages, such as Wengen ( my favorite) . I'd explore Thun before I'd explore Interlaken.
Read the pros and cons and recommendations here:
Wengen draws enthusiastic fans:
Beatus Caves -
I have not been to the caves, but from what I can tell, they are much like other caves around the world. I've been saving them for rainy day, and always found other things to do, even after a dozen or so trips to the region. Never been there. We all have opinions. ;-)
One thing I am sure of. There is only one Jungfrau. I go with the attitude that I'd rather see the "Swissy" stuff.