Hi Ravenyan
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Buy 7-day JR Ordinary Pass (22,300 Yen)
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I'm assuming you don't know, but JR railpasses of any type cannot be purchased in Japan. As they are directed at tourists, you will have to buy the EXCHANGE VOUCHER in your home country, up to 3 months before you plan to use it. Once you need to use it, you go to a JR station to exchange the voucher for the actual JR railpass. (I can think of Ueno and Tokyo stations where you can do this)
Your itinerary needs a bit of work. You're not spending enough time in Kyoto, there's so much to see there! Also consider a day trip to Nara, ancient capital of Japan and home to the best temple complex I've seen so far.
Tokyo tower is a good place for the 'sky-high' views, also in the nearby area is Roppongi Hills, Tokyo Midtown, The World Trade Centre, Tsujiki fish market (which is already on your list)... Ginza was pretty 'meh' as far as I was concerned. Also consider Akihibara, as already posted...
That's all I can think of right now.