Where are you flying from? CO has non-stops from EWR and IAH to NRT, and you can also use CO points to book on NW, which has lots of flights to NRT, so you have plenty of options. The CO and NW flights are J only, not F, but it is still pretty decent. The other nice thing is that CO will let you hold the reservation for a couple days while the points transfer over from AmEx, so you aren't risking the seats disappearing while the points transfer; ANA will not do that. I doubt that you'll do better on the paid ticket + upgrade with miles approach.

No real thoughts on the hotels.