Japan trip may 2015

As is your travel comes up a bit short for a 14 day JR Pass, but with a few minor but worthwhile side trips you can easily cover the cost and broaden your experience.
One possible solution is to get the 14 day pass, and activate it on May 5th, using it to the end of May 18. On May 6th you could take a day trip to see Nikko. Another half day could be spent at the Ashikaga Flower Park which should be in full bloom for you and is stunning.

Also near Kyoto is Japan's finest castle, [Himeji] (http://www.japan-guide.com/e/e3500.html "Himeji") and its multi-year renovation has just been completed.

Since you are already seeing Tokyo, you can largely skip Osaka during the day. But at night the city comes alive and has some great places to see, such as Dotonbori, plus the night views from the Umeda Sky Bldg and Abeno Harukas Bldg are stunning:

https://www.youtube.com/watch?v=COJ_MeXbeow

https://www.youtube.com/watch?v=xb1wuyAGgyQ

https://www.youtube.com/watch?v=-AyUZmGbW8g

I wouldn't worry about booking first class green seats - you can do fine as is. But Golden Week can be hectic and your idea of reserving seats first makes sense.