Thank you all for your thoughtful advice, it's really appreciated.
A little background as to why we were thinking about driving rather than trains, which we're not totally opposed to. My wife has a prosthetic leg that doesn't really keep her down, but does limit the amount of walking she does. We were thinking that rather than having to deal with lugging bags (I have a RS softbackpack on my back and I pull her RS roller with one hand and keep my left available to offer her an assist when needed) everywhere, we could stash bags in the trunk, park and go on our way. If she is having a rough day, having a car allows us to easily modify our schedule to suit her needs.
Munich and Vienna sound as if they do present a challenge. Are there park and ride locations on the outskirts of the city that would allow us to hop on local light rail or trains for easier access to the city centers? I was even contemplating staying in place near the airport where we might have access to parking at a bigger hotel as a base of operation for those places, and again, using public transport to get around when in congested places.
We have not purchased our flights yet, but plan on doing so by the 11th (there are some really great deals going through then.) From Seattle, Frankfurt offers us a some direct options, which is why we thought about starting there.
acraven: yes, we plan on staying the first night in Frankfurt to rest first for exactly that reason. It worked well for us in Barcelona last spring. We should be in Frankfurt on May 4th and will look to fly back out (from somewhere) on May 16th.
Harold: It's not that we plan on avoiding all museums, but we saw plenty of art in Florence and Rome last year, so we thought we'd focus on other things (such as Mozarts Geburtshaus in Salzberg or say the The Hofburg Palace in Vienna) this time around.
I am headed up to the RS Travel Center tomorrow (a benefit of living in Seattle) to pick up the Germany, Austria and Czech books, which will also give us a better idea on where to firm our plans.
Again, thank you all for your insights and suggestions. We're certainly going to take all them into consideration to help make our trip the best it can be.
-Robert