I've been to Skikoku four times for about a month each time. As you are probably already aware the island is small and mostly rural. It is much, much different from the big island and the big cities. The place is ultimately civilized and polite. Honor is everything. Genereally, if you are quiet and polite, if they percive that you are making an effort to not be a jerk, you'll be fine. Try to learn a few words of japanese - if you haven't already.
Briefly, with respect to photography, if you are taking photos of just about anything other than people, you will not have any trouble at all. There will not be an issue with your tripod or any of your gear. You will never have to fear that somebody will steal something (at least none of the natives) nor will they be upset or tell you that you cannot photographe this or that...as long as there are no people.
You will need to be very, very careful about photographing people - especially in the smaller towns. The farmers and fishermen live according to the old ways and adhere to strong beliefs.
Respect and courtesy is everything. You will screw up - because thier ideas about what is polite and what is not are, in some cases, exactly opposite from ours. Don't worry too much about it.
It will be a fantastic adventure. I wish I could go back.
Oh, and if you get a chance go see the Akashi Kaikyo Bridge.