I would base in Oberammergau for part of the trip. You can leave Munich Hbf at 9:32 using a Bayern-Ticket, switch to a bus at Oberau, and get to Oberammergau at 11:19. If you stay here, it's a short walk to your accommodations; check in, leave your luggage, and get back to the station for the 12:50 bus to Wieskirche. That will give you an hour to see the church before catching the 15:00 bus back to Oberammergau (15:34). Spend the rest of the afternoon and evening exploring Oberammergau and having dinner. Note: there is really nothing extraordinary about Wieskirche. It's just like a lot of other overly gaudy Rococo churches in Bavaria. When I was there in 2007, I walked in, looked around for a few minutes, and retired to the Gaststätte across the street for lunch.
The next day, take the morning bus to Linderhof. I found the grounds fascinating and spent most of the day there. Some of the buses return to Oberammergau via Ettal. Guided tours of Ettal are only for groups, so you probably won't be able to see anything. It's a cute town for a quick visit.
The next morning, check out and take the bus at 9:30 getting to Garmisch-Partenkirchen Bahnhof at 10:16. There are lockers on the platform at the Garmisch-Partenkirchen Bahnhof. Stash you luggage there and walk over to the Zugspitzbahn Bahnhof and take the next train. Get off at Eibsee and take the cable car to the top. When you come down, take the train 21 minutes to Mittenwald.
It's worth spending the night in Mittenwald. It's not a big town, but enjoy the ambiance There is a nice pedestrian shopping street with plenty of restaurants.
The next day, take the train from Mittenwald to Berchtesgaden (change at Garmisch-P, Munich, and Freilassing). That will take almost 5 hours. Take an extra hour and have lunch at the food court in the Munich Hbf. I would spend*** at least*** two nights in Berchtesgaden, there is a lot to see there.
So that's Oberammergau, 2 night, Mittenwald, 1 night, and Berchtesgaden, 2 nights.