Tips on Japan

Hello All
We're planning a 2 week jaunt to Japan next Easter, and can see UC reward seats exactly 2 weeks apart on dates which are OK for us. Unfortunately due to my OH being a teacher, the only other dates are when she needs to be at work or unavailable at the moment (weekends).
I'm looking for any helpful V-Flyer tips on our itinerary. We'd have 13 nights in Japan due to the overnight flight on the outbound.
We will definitely be getting the JR Rail pass.
Rough plan is:
- 4 nights in Tokyo (perhaps include a day trip to Nikko)
- 2/3 nights in Kyoto
- 1/2 nights in Mt Koya/Japanese Alps etc.
- 2 nights in Hiroshima
- 2 nights 'spare' perhaps Osaka/Mt Fuji area.
One slight issue is that VS fly in/out of Narita (nowhere near Tokyo itself!), therefore we've got to get back there in time for an 11.25am flight home. This would seem to necessitate either bullet training it up to Tokyo and one night in the city before traveling to Narita the next day, or perhaps we could get a connecting flight from Hiroshima/Osaka? There seem to be flights with ANA which allow a 2 hour-ish window. We don't really fancy ending our trip with a night in an airport hotel.
Any help or advise is much appreciated y)

We're planning a 2 week jaunt to Japan next Easter, and can see UC reward seats exactly 2 weeks apart on dates which are OK for us. Unfortunately due to my OH being a teacher, the only other dates are when she needs to be at work or unavailable at the moment (weekends).
I'm looking for any helpful V-Flyer tips on our itinerary. We'd have 13 nights in Japan due to the overnight flight on the outbound.
We will definitely be getting the JR Rail pass.
Rough plan is:
- 4 nights in Tokyo (perhaps include a day trip to Nikko)
- 2/3 nights in Kyoto
- 1/2 nights in Mt Koya/Japanese Alps etc.
- 2 nights in Hiroshima
- 2 nights 'spare' perhaps Osaka/Mt Fuji area.
One slight issue is that VS fly in/out of Narita (nowhere near Tokyo itself!), therefore we've got to get back there in time for an 11.25am flight home. This would seem to necessitate either bullet training it up to Tokyo and one night in the city before traveling to Narita the next day, or perhaps we could get a connecting flight from Hiroshima/Osaka? There seem to be flights with ANA which allow a 2 hour-ish window. We don't really fancy ending our trip with a night in an airport hotel.
Any help or advise is much appreciated y)