Greetings, what a wonderful site. We arrive on 30 September for a 6 week trip, in and out of Tokyo. We prefer to travel independently and at a leisurely pace. Our current thinking is to spend all our time in the central area including Tokyo, Kyoto, Osaka and surrounding locations like Hakone, Yokohama,Kawaguchico,Nagano, Takayama and Shirakawago etc, any place that is traditional, or quaint that we can explore and have the time to feel the true essence of. Of course we are open to any suggestions, and like the idea of multiple nights in locations where recommended.

My questions are:
is 6 weeks a nice amount of time to enjoy these areas.
Can we travel at leisure and book our accommodation as we go, ie air bnb, so we can stay longer in the locations we enjoy.
Can we use local transport options rather than face the restrictions of using the JR pass only, or have a combination of both
We will probably spend the most nights in Kyoto
I Hope I haven’t asked too many questions
Any advice would be greatly appreciated
Thank you

All of those places are pretty well-touristed, especially Kyoto, and maybe except Yokokhama. You can take a look now to see what\ lodging availability is like for your dates. You will probably find lodging difficult to come by and expensive in Kyoto for the last two or three weeks of your trip.

IDK about air bnb but there is a basic hotel style called a business hotel that used to be easy to book, but are tiny and meant for an overnight stay (by a business person visiting). Tourists are how using them, as well as capsule hotels, for longer stays.

Without a plan you probably don't need a pass. I would use a travel agent at a JR station to book loding if I were winging it. But I would not be winging it in that region these days, especially from late October into November (by :that region" I mean the whole middle part of Honshu).

https://www.japan-guide.com/e/e2014.html

Your trip is during Koyo time - autumn leaves - see above site for information about viewing areas and dates. So you might need reservations....
I usually go to Japan in the spring for a long trip and I always get reservations in advance...sometimes long in advance. Usually hotels don't require pre-payment so that makes it easier if you want to change your plans. Of course, airbnb requires immediate payment as far as I know.
Enjoy!!

The yen is weak because of Bank of Japan monetary policy. The exchange rate (for US dollars, at least) won't get much better than it is today (146.5) but it could drop 8 or 10 percent. That is what happened last November when the rate was approaching 150 and they freaked. BOJ made noises and did something about policy and the yen strengthened somewhat significantly overnight. Not that an increase would make a difference but I like a great deal and was a bit miffed when it only became a really good deal (135-ish),

The weak yen means more foreign tourists but it also means that Japanese are finding foreign travel too expensive. Result is an increase in the number of Japanese tourists in Japan (i think the domestic travel incentives have ended - that was vouchers and payments/rebates from the government). China recently permitted citizens to book foreign group travel tours.

For that reason, these days I am happy to pre-pay for lodging that that can be cancelled and refunded. At japanican I booked a ryokan that was pay now for November 1 and cancel by Oct 28 for a refund.

You can probably find some lodging that is a bit out of town and commute to the tourist sites (Kyoto and Tokyo). When the exchange rate was 105 yen/dollar I stayed next to Yokohama station to get a break from Tokyo hotel prices. Going up to Tokyo was a PITA but might be worth it for a long stay.

November 3 is a not-insignificant holiday (am seeing flights are sold out for Nov 2-3).