I wonft comment on your itinerary per se, but will share a couple of lessons I have learned in recent years:
(1) You may already know this, but when you look for hotels (or cheaper forms of lodging, but especially hotels), make sure you see a breakdown of costs per night before you choose (or eliminate) a particular property. Nearly all lodging establishments have a Saturday night gupchargeh, but the degree to which it varies by property is quite significant. Ifve seen places that have extremely low rates on weeknights but then the rate is triple for Saturday! On the other hand, a few places only charge 15% more for Saturdays, or sometimes (rarely) even have the same rate all 7 days of the week. (As for other non-Saturday nights, the variations can be significant; sometimes Friday is also quite high, sometimes Sunday is lower than Monday, etc.). The point of all this is that if you find a property you like but the total cost is above your budget, look at how it breaks down before you rule it out entirely. In planning an upcoming trip, I have been carefully gdodgingh Saturday upcharges (which quite naturally tend to be higher in popular tourist destinations), and saving quite a bit of money as a result. I donft like making a lot of hotel changes and I prefer to stay several nights in a row in one place (which means I donft like to change just for a Saturday night). But if tweak my itinerary to adapt to the hotel situation (rather than fixing an itinerary in stone and then trying to find cheap hotels for those cities, regardless of day of the week), I can save money. It becomes quite a puzzle if you want to spend time in places like Fukuoka (or especially Kyoto, Tokyo, and Yokohama), but if your lodging budget is that low, it could be helpful. Another trick is to stay in places that are off the tourist radar map but close to a JR station, especially if you have a rail pass.
I have found that some booking sites donft reveal the cost per night for the rooms; they only give you a total price for the stay. I find this maddening, and donft even use those sites to look for hotels.
(2) Although it might seem more efficient to have one large suitcase, it is a lot easier to have two medium suitcases, for example a medium rolling suitcase plus a duffel bag or large tote bag with a gsleeveh that makes it easy to put it on top of the suitcase and roll around. On the shinkansen, if you have too large a suitcase you have to reserve a space for it, and even if it is below their limit so you donft need a reserved space, it could be hard to get onto the luggage shelf above the seats (it might fit, but could be very heavy to lift). Large suitcases can also be very unwelcome on local transit such as commuter trains and buses. Also, it can be impossible to find coin lockers that will hold a large suitcase. And if you have two pieces rather than one, it is easier to occasionally use takuhaibin (luggage delivery service) to get some of your stuff out of your hair while you are traveling around. Of course, you will want to make sure your airline gives you two free checked bags, but many of them do.
Regarding rail passes, I have spent hours (and hoursc) analyzing the various regional passes including the JR West passes and the JR Kyushu passes, and finally decided that for my upcoming trip the nationwide pass is the winner hands-down. Of course you would want to buy it before October 1. But it wonft be for everyone. Using regional passes and flying from Kyushu to Tokyo is indeed an attractive option, not only because of the low cost of the airline tickets but because of the time saved. But be sure the fares you are seeing are actual, bookable fares on dates you really want, and also donft count on low-cost airlines (or even regular airlines) to get you to Tokyo just a day before your flight. Even trains can be impacted by bad weather, but planes are especially vulnerable. Low-cost airlines are notoriously unreliable anyway.
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