Hello again,
Looks like you are researching your trip very well, hope I can add to it.
1.) Seat reservations with the JR-Pass are completely free, if you don't have a JR Pass seat reservations generally are 250 Yen for a short trip or 500 for longer trips.
2.) The JR Staff will be able to make all the reservations for you once you exchange the JR-Pass, however you are not bound by them. Meaning that you can make changes whenever you want during the validity of the Pass. To do this simply go to a ticket office, bring your JR-Pass and previously booked tickets. Please return to tickets to the JR-Staff so they can free up the seats for other customers and make new reservations with the JR-Pass, this is completely free!
3.) This is an oddity I don't really know how to explain, for traveling to Hiroshima please use ''Hiroshima " as destination in Hyperdia.
4.) I don't have a station map of Kobe station but it is a very small station, so it won"t be hard to find anything. If you want to visit Kobe you probably want to go the station called Sannomiya as this is in the center of the city.
5.) You won't be able to use the pass from Gokurakubashi, the closest station to Koya san is Hashimoto, you can use the JR-Pass to travel from there!
6.) Osaka is a very large city and has many local stations. Osaka station itself is very close to Umeda, Shin-Osaka is from where the Shinkansen depart.
7.) Yes the Hakone pass works great to compliment the JR-Pass. For instance you can take the Bullet Train to Odawara and from there travel on my Hakone Pass without having to buy anything else besides the passes.
8.) Nikko can be reached by the JR so you won"t have to buy any additional passes. If you plan to visit it outside of the period that you use your JR-Pass you can save some money by buying a special package for Nikko, as mentioned before.
9.) You can"t buy these passes over the Internet but you can buy the Hakone Pass from Hakone or Shinjuku when you go to Hakone. You can buy the Nikko package at any of the Tobu Railway stations.
10.) You can maxiise your travel in Tokyo by trying to find an accommodation close to any station that is on the Yamanote-line this line makes a loop through Tokyo and stops at many of the great wards, including Shinjuku, Harajuku, Shibuya, Ikebukuro and Ueno.
11.) We had a similar question like this some time ago and Mari posted a great answer. You can find it here.
Let me know if you have more questions!
-Daniel
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