Our trip did feel a little bit rush, but I think that was mostly just because we underestimated travel times by a lot. Without going into too much detail right now, our trip went something like this: Day 1: Land at Narita Airport around 3 or so, get the train straight to Kyoto, arrive at our ryokan around 8 or 9, and go right to bed. Next, we spent a day each seeing Nara, Osaka, Eastern Kyoto, and Arashiyama. Got up early the next day to get the shinkansen to Hiroshima and saw the Genbaku Dome and Peace Museum, but all 4 of us felt the strains of exhaustion (sore back, sore feet, headache, and fever) at this point and we had to cut our sightseeing short to get to Miyajima that night. Saw the giant Torii at Miyajima the following morning and almost immediately left for Matsuyama. All told, that leg of the trip (ferry, train, streetcar, other ferry, bus) was probably close to 8 hours, so we couldn't do much there other than the public baths. Left early the next morning for Himeji. Took most of the day getting there, cause Matsuyama is very out of the way, so we didn't actually go to the castle until the following morning. From Himeji, we went to Tokyo, where we spent the last 4 or 5 days.
We did all that in about 2 weeks, and it sounds to me like you're not going to Matsuyama, so I see no reason you can't do all the other things you want to do. My personal advice is just to leave yourself one day to relax, whether it's just taking a walk around downtown or spending half the day sleeping.
If you want to get an idea of travel times yourself, the two sites I use the most are JR Hyperpedia and Jorudan. I may have spelled those wrong, but if you do a Google search for those you should be fine. And as far as lodging goes, we've only stayed at ryokans, so I don't have an opinion on hostels, but if you do opt for a ryokan, we do all of our booking through japaneseguesthouses.com.
I think I covered the most important basics for before you get there, but if you want to talk more, you can also email me at pagano dot brian at gmail dot com (sorry for spelling it all out, but I'm paranoid about spybots sending me junk mail).
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