Do you have the HHonors American Express? That offers the AXON award, 4 nights at Category 5 or 6 hotels / resorts for 125,000 points (same stay would normally require 140,000 or 160,000 HHonors points.) This allows you a bit more mobility, and there is a lot to see in Japan!

You might walso want to think about an open jaw flight, arriving via NRT / Tokyo, say, and departing from KIX / Osaka. This saves you from backtracking.

I don't know anything about your preferences, but I'd book a stay at Hilton Tokyo, and see some of Tokyo and surrounds - maybe a day trip with great walking to see the incredible temples complex in Nikko, as well as some local stuff.

Kyoto and Nara would be the other place to sightsee, and Hilton Osaka would be your hotel there. Getting there by Shinkansen train would add a dimension to the trip.

I highly recommend getting a general book that has information and photos, like the National Geographic book, or possibly Dorling Kindersley, so you can look and see what kind of things you want to do and see. Japan is small, but incredibly diverse - alps? temples? high tech? night life? You name it, it's there.