1) and 3) must use Google MAP ,
If the road has a light pink color, it means underground station.
At the big terminal station, you can see the inside of the station by Street-view of Google MAP.
2) has been calculated in average speed, so it is in time,
but if you don't understand the rayout of the station, you may get lost.
Also, although train announcements using English after Japanese as automatic broadcasting,
but individual transit guidance by conductor is only in Japanese usual,
however, it will be easy to understand if you pay attention to some basic words and counting,
taransfering is "o-norikae(‚¨‚Ì‚è‚©‚¦)" (first "o" means a word of plite),
"For xxx" is "xxx-iki/yuki(xxs‚«)", track No. is "xx-ban-sen(xx”Ôü)" or "xx-ban-noriba(xx”Ô‚Ì‚è‚Î)",
time counting is "xx-ji(Žž, =o'clock as 24)" and "xx-hun(•ª =min)", so Let's remember from 1 to 59,
if track No.4 is "yon-ban-sen/-noriba)", if No.7 is "nana-ban-sen/-noriba".
if arr(“ž’… : touchaku) 13:59 is "juu-san-ji : go-juu-kyuu-hun", if 14:00 "ju-yo-ji choudo(=just)".
https://blogs.transparent.com/japanese/japanese-numbers-1-to-100/https://youtu.be/sv0t0K24EI4This is sample of transfering guide annoucement, you can read already, right?
https://youtu.be/bBWFI_UMs98https://youtu.be/qPj9V8219Sg(small note)
Some stns have "No.0" but 0 is also called same "zero", but this is rare case no worry.
JR Kyoto :
https://goo.gl/g7FQypJR Matsumoto :
http://www.jreast.co.jp/e/stations/e1444.htmlIn Japan, like "London King's Cross railway station" in "Harry Potter", no such "No.9 3/4" tracks :)
4) is not for all JR trains, (mentioned already by above answerists)
and trains that can be booked online in English are limited.
"JR" is not only one company 6 exist, but they have English pages in all, open their web each.
http://www.japanrailpass.net/en/index.html (remember 6 colors, if through Japan N to S wide)
5)
HyperDia is convenient for long distances,
also especially for Japan Rail Pass holders, but there is no function showing route map.
Google MAP is also convenient for middle/short distance searches,
but there is no function to change the setting in detail,
such as "JR" or not, "reserved seat" or not, sort by fare fr cheapest, and more,
always shows "fastest time" plan, this is not for good case a lot.
(if you have a cellphone or tablet PC with app og G, you can search by voice "from here" like this.)
https://youtu.be/teypN6V6PsMAnd, both use the official timetable of the railroad company,
but do not correspond to the delay information.
Also, for looking for transfer station maps, there is only a part of the major station a map of English,
so you have to use "image search" of Google with "station name(in JP, kanjij xx‰w + \“à}".
The Japanese(written in kanji) of station name is easy to get at "wikipedia(English version)",
even by image search of G, but it is easier to use wiki for C&P.
(if look for "Hiroshima stn/-eki" of JR-WEST, input "L“‡‰w \“à}", no need "+", just put a "space")
https://en.wikipedia.org/wiki/Hiroshima_Stationhttps://www.jr-odekake.net/eki/premises.php?id=0800613Anyway, many Japanese who are not used to traveling in Japan are confused usual,
so it will be tiring if thinkin' too much/busy plans.
Result of HyperDia is correct or not, someone can be answered immediately if you post here ASAP.
But regrettable that the Q is not reflected in real time in this forum.