2 Week Japan Itinerary

Just started putting together the deails, it's still a rough draft. We will be going around April of next year.

1 - arrive in tokyo
2 - day in tokyo
3 - day in tokyo
4 - day and night in osaka
5 - osaka and mount koya with overnight temple stay
6 - day in hiroshima
7 - day and overnight camp at Miyajima
8 - day in kyoto
9 - day in kyoto
10 - kyoto with day trip to nara
11 - day in tokyo
12 - tokyo with day trip to nikko
13 - tokyo with day trip to kamakura
14 - leave from tokyo

Your itinerary ignores travel times between cities:

For example, you will spend half of your day 6 with traveling from Koyasan to Hiroshima. Consequently, you will have only half a day at Hiroshima, at best. Furthermore, in order to have any time to see Koyasan itself, you will have to leave Osaka for Koyasan in the morning of day 5, leaving you with not much or no time to see more of Osaka on day 5.

Don't under-estimate the time it takes to travel between the cities.

Good point. Is it possible to travel overnight or really early in the morning and sleep on the train?

If you were to use night trains as accommodation, you have to consider moving around your itinerary. The idea is going back and forth Tokyo and Osaka using the night trains. Use the SUNRISE SETO and IZUMO.
You are right, it gives you a lot more time during the day, but quite exhausted on the other hand.
However, I really recommend this mode of travelling because it is very fun and good for the experience. I did this twice a year using the JR pass.