Hi Renato,
For Kudanshita, you can use the JR Pass to get to nearby Iidabashi, where you can transfer to the metro for the 1 stop south to Kudanshita on the Tozai line (¥160).
You should be aware while Yokohama stadium is accessible from Tokyo very easily, Toyota stadium is in Nagoya and is a 2.5 - 3hr trip by bullet train and local trains from Kudanshita. You can see more on the options for getting to Toyota stadium from Nagoya here, but for the matches at Toyota stadium I recommend staying overnight in Nagoya as there will not be any trains running after the game to get you back to Tokyo.
For Yokohama statium you should aim for JR Kannai station. I recommend travelling to Akihabara and then transferring to the JR Keihin-Tohoku/Negishi Line Local all the way down to Kannai stadium. Here's a sample itinerary for you. For the journey back, you can follow a similar path (or perhaps change at Kanda also). Here are some sample itineraries departing at 10pm and 11pm. Be careful here as the last trains that can get you back to Iidabashi will leave Kannai station at 23:37.
Mt Fuji (Via Odawara/Hakone), Kyoto, Osaka and Hiroshima can all be reached with the JR Pass. Note that visiting Hakone will require you to purchase tickets on the non-JR Odakyu lines up to Hakone from Odawara. I recommend the 2 day Odakyu Free Pass for this and spending the night in Hakone if you have time. Here are your costings for comparison, assuming you'll be returning to Tokyo for your flight home:
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Tokyo > Odawara: ¥3,840 (35mins, 83km)
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Odawara > Kyoto: ¥11,950 (160mins, 429km)
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Kyoto > Osaka: ¥540 (28mins, 42km)
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Osaka > Hiroshima: ¥10,150 (104mins, 345km)
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Hiroshima > Tokyo: ¥18,250 (292mins, 894km)
JR ticket cost: ¥44,730 for 5 legs
Recommendation
It looks like you will make good savings with a 7 day JR Pass so I can certainly recommend this option.
If you intend to watch any games at Toyota stadium you will need to travel and overnight in Nagoya as there are no trains back to Tokyo at that time. Depending on which games you were attending, you could possibly structure your travel around Japan to match these games, however the final is in Yokohama so you will need to bear this in mind.
If you let me know the dates/places of the games you are thinking of going to I'll be able to help you plan your itinerary if you'd like?
Hope this helps!
