The tour to Cooktown (and its museum) would no doubt be very good, especially if it takes both roads, however I think with a three-day trip it is out of reach. Concentrate on a Reef Trip, possibly Kuranda, Port Douglas, and a Mossman Gorge / Daintree Rainforest / Cape Tribulation tour (or a rental car).
I've been to the museum at Kanchanaburi in Thailand - pretty moving place.
There's several museums in Kanchanaburi town and the one at Hellfire Pas that is manned voluntarily by Australians. You need to be there on Anzac Day. Can't move for Australians.
Good place also to swim in the river if game and not scared of the monitors.
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