What everyone else said, except malaria is a possibility on land (I got two bites sleeping in the hotel) though mosquitos didn't typically make it out to the boat though we anchored relatively close to land.
You shouldn't need much/any money on the boat as we didn't stop anywhere for land tours or visits.
I'd suggest Nitrox for the extra safety factor.
Unless you are ready to dive right into Indonesia food, then bring something like oatmeal or something you like for your first breakfast in the hotel. Food is excellent on board, with mostly Western but with more and more Indonesian flare as you go on. Enjoy the spam sandwich or KFC on the flight to Sorong.
Bring an open mind.
Definitely get a guide and driver. Likely any decent size hotel can suggest one. You'll see much more and get a lot of info. Ours charged $40 for the whole day. We gave him $60. In addition to where you want to go, they will take you to the wood carvers, stone carvers, and silversmiths, that they know, but, they do have excellent quality.
We stayed in Kuta which is in the city near the beaches. You can also stay out further such as Ubud, where the rice terraces are. You can see the monkey Forest, which is good if there aren't many people around to get them excited. Remember, the monkey touches you, you don't touch the monkey.