My friend and I did the exact same route over the same timespan last Sept. We went from Munich, down the Isar to Bad Tolz, then joined the Bodensee Koenigsee radweg to a little town called Brannenburg, then up to Chiemsee (the ride along the south of the lake is not too pleasant, you follow the autobahn, but once you turn North, it's very nice, flat land quite at odds with Bavaria), then from Chiemgau to Berchtesgaden (which was actually a bit rough - would recommend Bad Tolz which is a few miles before it and much nicer), then had a nice ride to Salzburg. We didn't do as many miles as you want to do each day. First day about 60, second about 60, then maybe 45, then 50, then maybe 35. We took time off in Salzburg, then caught the train back to Munich for Oktoberfest.
On reflection, talking about it later, we think we should have gone straight for Salzburg instead of Berchtesgaden, then cycled back to Munich, stopping somewhere in between. Trouble is, the towns get really small, and accomodation can get a bit sketchy.
If I did it again, I'd wild camp. Plenty of land out there, plenty of forest.
Here's a list of the hotels we stayed in, and the prices we paid for a double room:
4 you Munich £72.36 (Hostel - okay but a bit of a small room)
klammerbrau bad tolz £63.39 (Nice hotel - room a bit old fashioned, but big)
Schlosswirt brannenburg £69.38 )great room, quiet location)
Unterwirt chiemsee £58.58 (great hotel, though room a bit small)
Unfortunately I've not got the info for the Salzburg hotel, as my friend booked it. It was across the river in the Neustadt, and was in a hotel which had great food and its own brewery. Nor have I got the other Munich hotel we stayed at the last night. The prices were pretty much on a par with above, though.
Hope that's a help.