We have been planning a similar trip... about two weeks, one week in each city.
We will do the trip independently (not an organized tour). But we probably will take a guided day tour or two to some specific destinations that are far outside of the cities.
For arrangements I have been looking into Gate1Travel. They offer full guided tours, but they also have a build your own (independent) vacation tool on their web site. It looks like they allow independent vacation customers to book their day tours ala carte.
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