Three guys, three generation trip (From 67 to 11 years old) trying to get some gaps filled in our plans. We will be leaving in mid March 2020 for 10 days in country. Like many of the itineraries I see we will do 3 full days in Tokyo and 3 full days in Kyoto. Nara and Himeji will be either from Kyoto or as afternoon or morning stops while in transit. I'm trying to balance out some other ideas probably a little further out of big cities. I am curious about the whirlpools in Naruto and the vine bridges of Iya Valley. It's kind of a hodge podge of questions but I will list my thoughts.

1. Is it conceivable to fit in my Shikoku destinations between Tokyo and Kyoto? I know that transportation will be a bit slower as I get more remote. Are there other interesting things along my possible routes that might interest the 11 year old. Is there any public transportation to the more remote bridges in Higashi?
2. Is the Mt Fuji area worthy of an afternoon and night in March. We won't have time or probably the weather to hike.
3. We will consider JR passes once we move out of Tokyo. I assume you can jump off the train if a town seems interesting and continue to the destination if you have a pass. If you buy a ticket are you committed to a certain train or can you hop off as long as you don't change the ultimate direction to the end point on the ticket?
4. How common are non smoking lodging arrangements? Do they smoke on trains and busses?
5. Has anyone taken the "carpet bunks" on the overnight train from Osaka to Tokyo? I often enjoy the offbeat things that many traditional travelers would never consider.
6. Do all cash machines give the same exchange rate or convenience fees?
7. The younger folks are headed home and I plan to extend a few more days. Has anyone on the forum done the bicycle ride Shimanami Kaido?

Thanks everyone. I will enjoy your responses and probably have follow up questions.

I can only try to answer a few of your questions.

First, your itinerary. I'm not sure what makes you think that 3 days in Tokyo and 3 in Kyoto is common. 3 days in Tokyo for a first visit is reasonably common. Many people prefer 5, or better 6, full days in Kyoto for a first visit.

And that means that trying to fit Nara and Himeji into your time while in Kyoto and/or while in transit is ambitious. Doable, but ambitious. And FWIW, although many people visit Nara as a day trip from Kyoto, I was glad to spend 2 full days there.

I don't know Naruta or Iya Valley, so no comments.

1. I have no personal information. See japan-guide.com as a start.
2. Your call.
3. I don't know -- consult japan-guide.com
4. See this link at japan-guide: https://www.japan-guide.com/e/e2228.html
5. Not I.
6. No -- it depends on YOUR bank and the networks involved (your bank's network and the network with which the ATM is associated. In general, the best starting point for info is your bank.
7. Not I.

Good luck obtaining the rest of the information you seek! IME, japan-guide is a great resource -- just type what you want to know in the upper right by the magnifying glass. And you can post questions there, too.

Well actually, according to your plans so far, that just leaves you 4 days besides Tokyo & Kyoto. It would take you over 4 hours to get from Kyoto to near Iya Valley by train. If you are not renting a car in Shikoku, things get extremely slow and time consuming.
The Fuji 5 Lakes area has some pretty good sights to see. If you have the time and interest, it is well worth going. You don't list your whole itinerary yet, so it's premature to think of getting any JR passes. Are you leaving Japan from Tokyo or Osaka? With the pass, you can hop on and off as much as you like. It might be better to get a regular fare ticket from Tokyo to Kansai, and then use a regional pass...but you still have some itinerary to decide. Smoking is not allowed on the regular train cars. The bullet trains have some smoking areas that are shielded off. There is no smoking on buses these days. I haven't taken the sleeper trains - they are almost extinct..
For "cash machines" I presume you mean the ATMs. Each bank has it's own rate, but they are not far apart. For 7-11s and Japanese post offices, the only charge you get on the Japan side is 110 yen for a 10,000 yen withdrawal, and 220 yen for 20,000 or more. It's what your bank charges at home that really gouges you. My big rip off bank charged me a $5 out of network fee, a 3% foreign exchange fee, plus the spread from the interbank rates as their pound of flesh. If you have your money in a credit union or Schwab account you get low to no fees at all. My CU charged me a straight 0.8% and that was it. The ideal way to pay though is if you have a credit card with no foreign exchange fees. Not every place takes credit cards though, that said, more do these days. There are also some Family Marts and Lawson's which are increasing their foreign card ATMs with the glut of people for the Olympics coming. Just make sure you notify your bank first before departure so they don't suspect fraudulent usage and freeze your account.
I have not done the bike tour on the Shimanami Kaido - though many I know loved it. The Kosanji Temple along the way is tremendous.