Since you are there in August, the shinkansens are going to be very crowded with all the families traveling on holiday (kids are out of school in Japan only in August), especially in the morning and evenings when the business traveler is on the move too... My experience is that the green cars always have seats available, even in the worst rush hours.

If it is not too late, you might consider heading out of Japan from Osaka-Kansai. Most airlines consider NRT/KIX to be co-terminals (at least UA does), and it appears you are in business class so this gives you some flexibility, I believe. If so, just visit Tokyo first, then buy your one-way shinkansen ticket(s) down to Kyoto, Nara, and then head home from KIX. It is much less than the JR pass (probably set you back $150 or so).

If you are a fan of the IC Hotel Group then I highly recommend the Intercontinental Tokyo Bay. The rooms have fantastic views of the bay and the beautiful Rainbow Bridge. It is quiet, quiet, quiet (except for the occasional fog horns of the ferries coming in to port.... I love it!). You are just a quick 10 minute hop to Shinbashi via the connected Yurikamome above-ground train line. From there the JR gets you to any of the major shopping areas. You can usually score a good room there for under Y20,000 per night on www.6c.com

Feel free to message me if you want more details.