Best route in my view would be as follows:
Munich - Salzburg (well worth a look) - Spend a day or two in the Salzkammergut/Dachstein region then head south to Bruck then Grossglockner ( Grossglockner High Alpine Road).
After the pass I'd recoomend heading east to Spittal and taking int the NockalmStrasse before dropping into Italy via Villach
Have you thought about going a bit further and going through Slovenia?? It is awesome and a couple of days detour will see you in the Julian Alps and then into eastern Italy.
I don't know Italy well for biking (I live in Austria) but when coming back up I would recoomend you take the route from Italy into eastern Switzerland - do the Stelvio Pass or BerninaPass. Once in Switzerland take the route east through the National Park from Zernez to Mals and then head form Innsbruck.
From Innsbruck you can go up through the mountians to Bavaria and then to Munich.
Alternatively, don't go as far as Innsbruck but head to Garmish.
Oh, and if anyone suggests go go to Augsburg - forget it- the place sucks!
Have fun.
J
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