I did the 2008 Oriana world cruise from Southampton to Australia. My husband and 14 year old daughter did not have any vaccinations. We did alot of excursions on our own but if you are going to Eygpt, although the excursion price is really expensive, I would still recommend to use the ship excursions if you want to see the Pyramids as it is 2 hours away where the ship docks and safer. Just do a google to the sights you want to see to learn how to get there by yourself, much cheaper and more fun.
Is the very early start and long day worth the Pyramids tour on Oriana or perhaps it would be better to save such a trip to a dedicated Egypt tour? Or did you hear from fellow passengers whether the cruise through the Suez Canal was interesting?
It is possible to do all ports by yourself if you do enough research....personally I would have been working on this for at least 6 months already getting it all organised! For a start go to a search engine and type 'asia message boards ports' and click on first answer returned. That will give you ideas for Asia and from that page you can naviage to everywhere else in the world.
As for injections, we are a group of travelagents and cruise enthusisasts - and not qualified to give advise - speak to your doctor/local health centre.