I think that I have finally figured out all of our hotel/B&B's. That took a lot of research on trip advisor and other sites, but all is done. We mostly went with bed and breakfasts. This gave us some nice places for reasonable prices as well as the convience of having breakfast included. We also made sure that most have wifi and all have aircon (just in case it gets hot).
Flights are booked - we decided to spend a little bit more so that we would only have one connection (long enough connection to make next flight hopefully) and stay with one airline throughout. We booked directly through the Lufthansa website, which as I said, was a little more expensive, but leaves me a less stressed.
Only thing left to book is any tours that we want to arrange ahead of time and tickets to museums. How much fun is that!!!