Planning a trip for 90 days, need help regarding purchase of multiple passes

Hi,

I am currently planning a trip to Japan, and would be visiting different places in Hokkaido, Aomori, Kyoto, Osaka, Tokyo, Kagoshima, Hiroshima, Fukuoka, Tsushima, Okinawa and Nagato. I wanted to know if I would be able to purchase a JR pass when I am already in Japan? If I need to buy a pass from my home country, I can do that, but buying all of the passes might be tough, as I do not have a concrete itinerary in place. I would primarily be spending my time around kyoto, osaka, tokyo and sapporo, and will visit other places from these points. If there is a way to buy the passes while I'm in japan, it would be great. If not, please suggest some alternatives, if possible.

Warm regards,
vjawsm