Thanks to everyone for the advice, much appreciated. I'm going to cut out Naoshima (or rather save it for another trip) and spend a couple of days in Tokyo and then base myself in Kyoto for the rest of the trip. I'm used to flying to Asia and jet lag doesn't bother me too much flying east, but you're right, the itinerary was a little optimistic!

gbs1112, do you have any suggestions for a nice ryokan?