[stuniq]

When you get there be flexible with your plan. You might find that it doesn't work out the way you want it to due to time constraints... so always know what your "must visits" are. I had a whole 3 week itinerary planned and pretty much threw it out the window when I got there because things didn't work out. So I ended up just planning the following day the night before. 3 sights a day usually worked out nicely for me. This gives you time to check out the place properly, enjoy the scenery, buy a souvenir and travel to your next sight without being stressed out when you're meant to be having fun...

It's also not a great feeling to be rushed getting to places and realising you have to leave ASAP. Having a JR pass is cool because you can travel all over for "free", so you don't have to worry about getting on the wrong trains etc. (besides the time cost). I would recommend getting the shinkansen JR maps and seeing what the most efficient route is. Also try to catch express trains that stop less (iirc).

I haven't been to all the places you're going but in Kyoto Kinkaku-ji, Kiyomizu-dera and Sanjusangen-do are great places to see. I had 5 days in Kyoto so I walked where I wanted to go (I enjoy getting the feel of the city this way), but for you I'd recommend the bus routes. The subway is very simple in Kyoto, nothing like Tokyo. So buses will get you closer to your destinations. Also get maps of the cities at tourist information when you arrive in each place.

I don't know the answers to your other questions.

Have fun!