Edward Enfield wrote a very good book "Dawdling by the Danube" which I recommend. In general, the area around the Danube, in Germany and Austria is quite scenic and frequently hilly so you will have no trouble finding alternative routes. In terms of accomodation, my experience is that there is plenty of accomodation available. Most towns will have a tourist information office which will help and can often book local accomodation for you. Just tell them your price range. In Germany there is an organisation called Bett und Bike which identifies cycle friendly accomodation.http://www.bettundbike.de/en
Lots of pubs do B&B. Look for the word "Fremdenzimmer".
The higher reaches of the Danube, in Germany are well worth exploring and can be fun, a pleasant change from the more manicured sections down stream.
Whatever you do, I'm sure you'll enjoy it.