Hmmm....don't have a map in front of me but i have cycled extensively in this region. What you want to see in Austria is the eastern border region called Burgenland. There is one extremely beautiful valley called the Hallental which you should see. Althought the 'alps' by this time have eased to big, green hills, the grades are very very steep. Maria*****nd is a maze of big green hills; although for some reason it always pours on me when I am on this region. The Ybbs river, further north near the border with Czech republic, is also nice.
These areas might be a bit off your route, as they are further east towards Hungary; but still well worth it.
The stuff you mentioned in Czech republic seems to cover it all very well. I don't do a 'route' when I am on a tour; i just head for the hills and go from there. Just make sure you drink as much Pilsner Urquell as you can. Be careful though...its 12% alcohol.
Roughstuff