Thanks for the replies. We can change the return from NRT to KIX (flights are available) but it will cost 90 Euros total. If you think it is worth it not to have to backtrack to Tokyo, I will ask AF to do that. It would also give us our fourth day in Kyoto which might make it worth it.

Four nights in Tokyo is really only three days and one of those days would be a day trip to Nikko. So that's only two days to explore all of Tokyo (museums, gardens, shopping etc.) If you think that is too much, we can cut it down. Maybe I figured that Tokyo had a lot to see and do based on the threads here in the forum.

After more reading about ryokans I am considering a side trip to Hanafubuki. On the way to Kyoto. It seems a little out of the way, but with the JR pass it seems doable. Again, the question is whether this should come out of our Tokyo time or our Kyoto time.

How is this for an itinerary?
Tuesday evening arr Tokyo, transfer to the Westin.
Wednesday, Thursday, Friday in Tokyo with one day trip to Nikko
Saturday midday travel to Izukogen (Hanafubuki)
Sunday mid morning Izukogen to Kyoto
Sunday p.m., Monday and Tuesday in Kyoto (side trips to Nara, Himeji) with one night at Kurama Onsen (?) and two (three?) at the Westin
Wednesday fly out of KIX

It looks a bit too ambitious now, especially since, as JR mentioned, it's really hot and humid in July which is something I don't handle well. Maybe we should skip Hanafubuki and just do Kurama. I know you can't decide for me, but I do appreciate input from those who know the lay of the land.