We've been to Sorrento and the surrounding area before so we decided to pass on Pompeii. Instead we took the Amalfi coast tour. It's breathtaking. We're not tour bus people but we felt it was the best option due to the amount of traffic you can encounter on the road as we didn't want to miss the ship.
We took the tour to Luxor and the Valley of the Kings. It involves flying 90 minutes south of Alexandria. While you have a limited amount of time in Luxor, and no time in Alexandria, you're still able to see the Valley of the Kings and the Temple at Karnak. By taking this tour, you don't have to consider making another trip to Egypt unless you want to do a more in-depth type trip.
We docked in Port Said. We arranged to have our own guide for the day. This allowed us to spend as much time as we wanted at the Pyramids. It also allowed us to visit the Solar Boat Museum. Since you're driving over three hours each way from the port, we only had a limited amount of time at the Egyptian Museum and no time for other sites. If I had to do it over again, I would still choose to do it this way versus on a bus tour where you're allowed a few quick minutes to see the Pyramids. Plus the price is about the same.
We docked in Haifa for two days. Initially we were to dock one day in Ashdod and the second day in Haifa but the port was changed due to problems associated with the second Turkish floatilla.
The port of Haifa is nothing special and we spent very little time in the city. Our focus was Jerusalem and Galilee.
We arranged to have our own guide in Israel. We spent the night in Jerusalem which is something I'd recommend because with the limited time you have on a cruise. You don't want to spend anymore time than necessary driving back and forth to the ship. This was especially true for us because Haifa is about two hours further from Jerusalem than Ashdod is.
I believe having our own guide allowed us to see much more than if we were on a bus tour. We were able to set our own pace which allowed us to see more. It's well worth the extra money if this is your first and possibly only time in Israel.