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Where to start my Japan trip?

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I'm headed back to Japan in October - some may remember that I limped round Japan back in 2010. I enjoyed it anyway and am looking forward to returning. That trip I visited Kyoto, Koya-san, Kanazawa, Shirakawa-go, Takayama, Matsumoto and Tokyo on Honshu, and Tokushima and Takamatsu on Shikoku. This trip I have a bit over five weeks, and I'm thinking of spending them working my way from Kyoto down to Okinawa, visiting both the San-yo and San-in coasts of western Honshu, more of Shikoku, and Kyushu, on the way.

I'll have lots of other questions, but right now I'm trying to decide where to start. I'll be coming from Busan, in South Korea, aiming to leave October 10th. I could fly into KIX, there's a reasonably cheap flight ($48) at a reasonable hour on Eastar Jet, an airline I've never heard of. I could take the overnight ferry to Osaka, although not until the 11th, arriving on the 12th. The trip through the Inland Sea is said to be scenic. A berth in a four berth cabin runs $145. In either case I would need to switch back and forth between the two coasts in western Honshu.
Or I could take a flight or the fast ferry to Fukuoka, which is $62 or $79 depending on the boat, and work my way up the north coast to Kyoto and back down the south coast. This would put me into Kyoto a week or so later.

Is Kyoto likely to be more or less crowded later in the month? I suspect I may run into the koyo season. Is it better to travel up the coasts, or switch back and forth?

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