I didn't read all of the above replys, sorry if this suggestion has been made allready:

Leave the Danube at Passau and cycle down to Salzburg. Then over to Munich. I haven't cycled the bit from Salzberg to Munich (took the train), but you should be able to piece together a rather splendid castle tour along the way. If inspired you could also include the "Eagles nest" as well.

Becnalls suggestion for cycling the Camino Santiago is also an excellent one, perhaps to keep in mind for your next trip if not this one. I pieced together my own route ("winged it") from Paris to Roncesalves, then simply followed the classic route to Santiago. Inexpensive, good food, excellent company from all over the world (both cyclists and trekkers).

~Cheers from Siem Reap Cambodia!~