Thank you for all the valuable information, we have booked the jungle train and amphibious duck tour in Cairns (extra fee) and the crocodile cruise in Darwin (free), we are open to finding private tours since in the longrun it will be a small added cost to the entirety of the cruise and also open to walking around on our own, finding restaurants in town, etc. I do hope they just reschedule the papa new guinea ports or change at least one of them. Unfortunately they changed Brisbane to Newcastle so I don't think the Australia Zoo is an option on our cruise. But the replies thus far have confirmed that we should be open to booking our own tours, not a big deal since the other things like food, service and room appear to be positive.