May travel

I am planning to visit in May with the following itinerary:
8 May - 11 May Tokyo then bus to Fujikawaguchiko
11 May - 13 May Fujikawaguchiko
13 May - Train from Mishima to Kyoto
13 - 18 May - Kyoto and visit Nara
18 May Train to Myajimaguchi
19 May train to Osaka
19 - 21 May Osaka and visit Himaji
22 May train to Kanazawa
22 May train to Nikko
26 May train to Tokyo
29 May Flight home

I think that I will not need to activate the pass until 13 May when I get the train from Mishima. I think that a 14 day pass would be best. Do you agree?
How easy is it to book seats? I think you cannot book seats until you have the pass in Japan is that right?
I am concerned I will not be able to travel on the day I want to.
Any help would be welcome.
Thank you