I think you have the right idea about combining your stops into 4 night central locations where you travel from that central location to the individual locations you are interested in. I think they combine easily into:
(Frankfurt?) + Rhine : 4 nights
Black Forest + Strasbourg : 4 nights
Bavaria+ Garmisch : 4 nights
Munich : 2 nights
Acclimatization - Having done a lot of international travel over the years the one thing that has helped me the most in adjusting to the new time zone is to immediately spend time in the sunlight. Rather than sitting on a park bench in Frankfurt (which is sort of New York on the Rhine) I would travel to one of the villages along the Scenic Rhine. We loved our stay in Bacharach, but there are plenty of other choices. We landed in Frankfurt in the early AM, picked up the rental car and were standing on top of the Lorelei by 11am - and I have no doubt the excellent German train system could have gotten us there just as quickly.
Depending on where you stay in the Black Forest you can easily take a day trip Strasbourg - or visit there during the travel from the Rhine down to the Black Forest.
I'm guessing 'Bavaria' = Ludwig II 'Castles' and mountain views? We found staying closer to the Alps gave us the views we wanted and the morning advantage on the 'bus people' coming from Munich. We spent 3 nights near Schwangau with a day for Neuschwanstein/Hohenschwangau, a day going to Linderhof & Oberammergau and a day at Garmisch.
I haven't visited Munich in years, but what I remember is excellent museums - history and science more than art, but maybe that was simply because I'm an engineer :-).
By flying into Frankfurt and out of Munich you can save half of a day of 'visit something' time. We actually flew into Frankfurt and out of Stuttgart last year and it was not only more convenient for our trip but also ended up slightly cheaper than a roundtrip through Frankfurt.
Sounds like fun!