Warnemuende is the port not only for Berlin, but also Rostock. If you decide not to take the long trip to Berlin, take the train from Warenemuende to Rostock, it's only about 15-20 minutes and costs about 5 euros. It goes frequently back and forth. The conductor helps you get tickets from a machine if you ask. There is a bank right at the train station to exchange dollars. Don't get off at the first Rostock stop, get off at Rostock Hauptbahnhof (main rail terminal). From there it's an easy walk into the city. Pick up a map at the train station.
In Stockholm, don't miss the Vasa Museum, take the hop on hop off bus instead of the ship tour and then you can stay as long as you like. The bus also drops you close to the Royal Palace and Gamla Stan, easy to walk around.
In Helsinki all ships have shuttles into the city, again, it's easy to walk around with a map from Information kiosk. Copenhagen the same, we walked everywhere. The Stroget is easy to find, great shops and restaurants.
In St. Petersburg we took the Red October tour and recommend them highly. It was the highlight of our trip, a bit expensive, but so are the ship excursions. RO got us to the front of long lines everywhere, right past ship lines.
We've been on many cruises, but enjoyed this one the most.