Sounds like you're doing the same itinerary I did a couple of summers ago. We didn't book any excursions through the cruise line, but did pre-book tours with local tour operators. Everything went very smoothly and we were very satisfied with our tours - plus we were able to get them customized to what we wanted to do and could stay as long or as short at any location that we wanted and didn't have to travel with a whole busload of other passengers.

I echo the previous poster's comment about checking out Cruise Critic message board. They have lots of recommendations for tour operators at each port. The European board can be found here: http://boards.cruisecritic.com/forumdisplay.php?f=19

Have fun on your trip!