I recommend
Hyperdia | 乗換案内 路線検索 時刻表 ゴルフ場 旅費精算 通勤費なら for any train schedule-related issues since you will be using the JR Pass. (It's awesome, btw! Used it myself)
Please reserve the Kyoto seats on the Kodama/Hikari service on the Tokaido Shinkansen as soon as you can, since it can get crowded without reservations and since it's included, so much the better! But if you're going to stop by Fujiyama on the way, perhaps the bullet train may not be the best way for most of the trip to Kyoto.
As for the itinerary, it all depends on what you want to see.
I'm sure others here will provide more, and better, input!
