We have just under two weeks to explore Japan, we land at HND at 7:30pm (JAL1) and will need to get cash, JR rail pass, mifi rental or sim (haven't decided what is better, sim is easier but mifi might be cheaper). I figure once all that is done it will be close to 9pm before we leave the airport? (accurate?).

From there we are looking for a good business class hotel that is easy to get to with luggage and on the train/subway for exploring.
Initially, I was looking at the Ginza/Toyko station area, but it doesn't look like the airport buses go there that late so we'd be looking at the monorail/train after 12 hours of flying. That might not be ideal from other reviews...

So I've started looking at the Shinjuku area and it's looking more promising, it looks like the airport bus runs at 9pm and there are a few business hotels with good reviews around the station (JR Kyushu Hotel Blossom Shinjuku or Hotel Sunroute Plaza Shinjuku or Shinjuku Washington Hotel, any opinions of those or others we should look at? The JR or Sunroute look like the closest to the station for exploring?)

We are thinking of spending 4 days (Jet-lag, getting used to culture, food, Studio Ghibli) in Tokyo before going to Toyama for 2 days in a traditional house, then onto Kyoto/Osaka as our next base for another 3 days (suggestions on best area to stay welcome), then back to Tokyo for a night (somewhere near the NEX?) before flying out of NRT at 6pm (JL68)

Also trying to factor in using luggage forwarding services as well (hence the day in Tokyo at the end)

Any feedback and suggestions to tweak the trip welcome