Don't have time right now for a detailed response - and am hoping for some others to chime in on some of the locations I don't know - but a couple of thoughts.

August in Japan is not autumn. It is the height of the hottest, muggiest, nastiest season imaginable. Autumn would be more like October or even early November. The best fall color photos I have ever gotten in Japan were in late Oct/early Nov.

As for routing, SFO to NRT is a good start. You could see Tokyo and the northern part of Honshu to start and work southwest to take in Kyoto/Nara/Osaka for several days and then continue "down" the island through Hiroshima/Miyajima and on down to Kyushu, then back to Osaka and KIX for the flight home. That would save backtracking all the way to NRT. You don't mention which airline you prefer but a few (UA comes to mind) fly KIX-SFO. Others will have a connection through either HND or NRT before continuing to SFO.

I'm still confused about destinations. You seem to be working down the island as I suggested but then, after Nagasaki (on the southern island, Kyushu,) you throw in Sapporo, which is clear up in the north on Hokkaido. That might be stretching things a bit. Frankly, I'd leave Hokkaido out of your plans unless you want to fly up there. It is a long way from Nagasaki to Sapporo.

My mention of Himeji was not to add it but rather to discount it. The only real reason to stop there is the famous castle but that is hidden behind construction scaffolding and tarps right now. Better to just blow right on through on the shinkansen.

My concern with ryokans, even the high end ones, is indeed comfort. The high-end ones you mention are wonderful. But from my perspective, sleeping on the floor and dining in-room are only nice occasionally, as a treat. I like beds and handy bathrooms too much to want to do that all the time. Others here disagree. YMMV.