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So I suspected. Are there any notable places where the JR Pass is unusable
(I imagine Hakone would be one? And I think I read here that in Kyoto buses would be the goto method)
JR pass pretty much won't cover anything that doesn't say JR on it. It won't cover Hakone once you get off at Odawara station. For Kyoto, you might use the JR rail once or twice to get to a sight easily (such as Fushimi Inari Shrine), but other than that, the busses are the way to go. You'll probably have mixed uses in Osaka depending on where to go and if I remember correctly, taking the bus in the Nara park area back to the JR Nara station was free.
Interestingly enough, any place that doesn't take the JR pass pretty much has their own day passes they sell. Hakone has their own 2 or 3 day pass called the Hakone Free Pass for 3,900¥ or 4,400¥. You can get different day passes for the Kyoto busses and there's also an 1 or 2 day Osaka Unlimited Pass that gets you free rides on trains and busses, free admission into tourist spots and also discounts for certain places.
I ate and ate and ate and I dropped 8 pounds on my trip. Walking and temple stairs.
Almost the same here, though I probably only lost 1 - 2 pounds at most. There pretty much wasn't a time during my 2 weeks there that I didn't have some sort of food on me or in my backpack. Every night when we got back to the hotel we would unload our backpacks and notice we had even more food.