Hi Pete, I recently came back from a tour that overlapped your itinerary between Innsbruck and Munich. You can see a map here:
http://trackmytour.com/5600. The via Claudia Augusta map I have doesn't put the route through Innsbruck; rather, it goes from Fussen to Reschenpass via Landeck. Either way, the path I did ride was very well suited for cycling. Have fun!