Hut to hut hiking in Bavarian Alps

We've done a lot of hut-to-hut hiking in the Alps but not in Bavaria. I took a second and looked up the Deutscher Alpenverein, the German hiking association. I can't believe that they don't have their website repeated in English! That makes it hard but you may be able to manage it...
Start at the Deutscher Alpenverein website.
Click on "Hutten Turen" at the left.
Then click on "Hutten" in small menu underneath it.
Then click on "Hutten suchen and finden".
Up will pop a map...if you click "Karte" at the top of the map it will show you a map with how many huts are in the different regions on the country.
If you click on the ones south of Salzburg and Munchen you'll be in the area of Bavaria.
If you find some you like you can go to "Liste", find the name, click on it, and it will show you the website for the individual hutte you are looking at. If you shoot them an email via "Kontakt" I'm sure they'll reply...I have yet to find someone who works in an alpine hut who doesn't speak English. They deal with people from all over the world and English has truly become the common language when people meet who don't speak the same language.
My only other advice would be to reserve ahead of time, at least for your first night. We have found that, once you show up at a hutte, they are usually happy to call ahead for you to reserve a place at the next hut. In summer, this can be risky at the smaller ones but if you join the Deutscher Alpenverein, and if it works in the same way as the other associations in Europe, they usually set aside a block of beds for members of the association at a better price than the general public.
Also ask if they provide bedding...many (most) do but there are some at higher elevations who can't since they don't have water to do laundry.
I know that isn't exactly what you wanted but I hope it at least helps you get started in the right direction!

Have a look here, the trips at this site are longer than 3 days but you may pick up some hints from the detailed trip notes on the RHS of the page.

If you use the search tool on the LHS side of the page and choose Germany and Alpine walking and any grading there are three other walks in the same area.

Happy travels.

Try this site: http://www.alpenvereinaktiv.com/en/tours/#filter=b-onlyTopTours-1&zc=10,11.53221,47.64596&cat=Mehrtagestour

It' where the DAV members post their own hut to hut tour (and other outdoor activities). There is several multiday hut to hut routes shown. For example here is a 4-day tour: http://www.alpenvereinaktiv.com/en/tour/4-tage-huettenwanderung-von-rottach-egern-am-tegernsee-rund-um-den-spitzing/8180649/

DJ