Sorong, Raja Ampet, Manokwari, Jayapura, Baliem Valley.

I am booked to fly into Jakarta 4thMay with my two sons, 12 and 15 who are into birding. I fly into Sorong and then I have a Guide for the birding who will do a 9 day tour with us of Raja Ampet, and Manokawri. From Manokawri I go to Baliem Valley without a guide and then fly back to jakarta 27th May. I have nothing planned for Baliem Valley.
Do you think I can also do the flight bookings once I reach Sorong?

Also I want to travel light and hate carrying too many shoes. Will water/trekking shoes like Keens work or will i need separate Hiking shoes for Baliem Valley?
Is there any other advice you want to give me? About permits, travel with kids etc?
Thank Gauri

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