I think your tour sounds excellent. Since you have a lot of time you should have a lot of flexibility to modify the trip as you go. I am sure you will see many other cyclists along the way that will suggest things.

If you want to see some of the Alps without a lot of climbing, follow the Salzach river from Passau to Krimml. Unfortunately you will then have to either retrace your steps back to the Danube, take the train, or climb mountain passes. Get the Bikeline or Schubert & Franzke guide for the Tauern bike path, both of which are available in English, and look at my writeup at http://webhome.idirect.com/~brown/austria1.htm

As becnal mentioned, the Bikeline guides are excellent. Most of them are only in German, but the maps are invaluable. They cover the entire Rhine and Danube paths, plus there is one for Bodensee and many other routes.