Ugh! It is always best to schedule the heavy travel days toward one end of the trip or the other to get the most out of the Japan Rail Pass. In this case, your heavy travel days fall in the middle. For the above, I think your best bet is to "activate" your Rail Pass immediately upon arrival and use it to "pay" for the first ride into the city on the N'Ex, all train travel around Tokyo for the first few days, the trip to Kyoto, the roundtrip to/from Himeji and the return trip to Tokyo. This will leave you to pay out-of-pocket for the roundtrip to Kamakura and the last N'Ex or Keisei line trip back the NRT for departure. Activating later, on the 1st, would cover the Kamakura trip but since the Yokosuka Line is less expensive than the N'Ex, you would be actually be losing money.

I suspect you already know, but just to be sure - - you cannot make your train ticket reservations before arriving in Japan but you MUST purchase and obtain the Japan Rail Pass voucher before you arrive. It cannot be purchased in Japan. If you are in a major city, you can purchase it at JTB or other travel agency offices. You can also purchase from some online sources and have it mailed to you. The voucher must be redeemed and used within 90 days of purchase, so you might want to start thinking about buying it a month or so out, although it typically only takes a few days to arrive in the mail.

JR