When you're looking at hotels, remember that the category of "business hotels" in Japan are not like U.S. business hotels. They're where junior staff stay - in small, clean rooms, not executive suites. Good bargains, but don't be surprised if you can touch opposing walls at the same time!

... with your belly.

Far better to stay at $hitty hotels. They're not at all like the $hitty hotels you find in the US.

I got a better one. During the 2002 World Cup, we went to the Mexico-Italy game in Oita, in the boonies in Kyushu. We had an extra ticket, so we sold it to a scalper outside, at face value. We knew that whoever sat next to us, would have bought the ticket from said scalper, and could tell us what kind of markup he was getting.

So this Mexican guy walks in and sits there. So we start the small talk, and it turns out he had landed in NRT the day before, rented a car in NRT, and drove from NRT to Kyushu, got to the stadium and bought the ticket from the scalper outside. Guy spoke no Japanese whatsoever, and had never driven on the left side of the road. Talk about a rabid fan.

So whenever somebody gets all hot and bothered about how Japan is so difficult to navigate, blah blah, I just tell them that story.

By the way, he bought the ticket at a small discount to face value, so the scalper actually lost money on the deal, good Karma for the buyer!

Monterey is a Japanese-owned and operated chain with somewhere around 15-20 properties. We stayed in their Kyoto property on the Karasuma-dori (the main street that runs away from the railway station); absolutely beautiful, wonderful and charming staff, and their own rooftop "onsen". The Kyoto subway had a stop about a block away. I think you can get a $150 per night rate there.

We did do a guided tour on one of our days in Kyoto, which hit the highlights in Kyoto in the morning and the highlights in Nara, about 40 minutes by road away from central Kyoto, in the afternoon. As we had been in Japan a week by this time and were pretty much worn out from all the walking we had done, doing a guided tour for one day was right for us (my wife and I are in our mid-50s).

A JR 7 day pass is worth it; we did the Green Car pass, and it turned out that the cost of the pass was only a few yen more than a single Green Car round trip from central Tokyo to Kyoto. Not only did we ride the Tokaido Shinkansen to and from Kyoto, we also went to Nikko (about 100 miles north of Tokyo and really worth a look), rode JR trains all around Tokyo, and I did the Joetsu shinkansen through the mountains up to Niigata and back, just to do it. There are plenty of on-line travel agencies that can set you up with the pass-they send you a receipt, which you take to a JR service center (there is one on the mezzanine between the arrivals exit in NRT Terminal 1 and the rail station platforms; another one is in Tokyo station), show the agent your passport, and they issue your passes right there (and make seat reservations if you want them; all Shinkansen green cars are all-reserved).

I love Japan; it is sensational. I've even printed out instructions on how to read and write the Hiragana alphabet, and even have picked up a few words (Kita is north, Higashi is east, Minami is south, and Nishi is west--how about that?). I'm sitting here looking at about Y8,500 that I had left over from my last trip--I cannot wait to go back.

Okay - time for an update from the OP:

Thought I had things pretty well planned out when I found out yesterday that my niece will probably be married over Labor Day weekend (when we planned to be there) so I was back to square one.

Finding flights was not easy and we ended up taking the only Business Class award seats we could find. That means we are flying Air Canada, leaving Sept 7th and arriving the 8th. The only seats I could get to return are on the 20th meaning we will be there a few more days than I had wanted.

Reserved the Ritz in Tokyo from 9/8 - 9/13. Contacted both the hotel directly and Ritz reservations and we have been upgraded to a Club level room with Club Access for an additional $100 per night above the Marriott certificate.

Also reserved the Hyatt in Kyoto from 9/13 - 9/18.

Question is what to do the last night? Do I add Hiroshima for one night (the 18th), then train back to Tokyo for the last night to rest and wait for the flight? Do I just add one more night to Kyoto? Any other ideas?

Many thanks for all the generous help.

Here's my suggestion - Reduce your Tokyo stay by one night (9/8 to 9/12). Make a two-day onsen trip after Tokyo - to some rural destination in the mountains (or Hiroshima if that's what you want to see). Then stay in Kyoto until the final day of your trip (9/14 to 9/20). Take the Shinkansen from Kyoto around 11am to connect to Air Canada flight 4 (Departs Tokyo at 5:30pm)

Or ... if you want to do a Hiroshima trip at the very end of your stay ... Take the train to Miyajima on 9/19. Stay overnight at Iwaso onsen. Visit Hiroshima in the morning of 9/20. See the peace park and museum. Take the bus to Hiroshima airport. Catch ANA3114 to NRT (Departs at 2:25PM). Connect to your flight home.

Japan is my favorite place. You could also do a day trip or overnight north to Nara. (it's about an hour on the direct train, but the direct train is not JR (if I'm right), so it's a separate ticket). I love Nara. It's got tons of temples, they are close together and they are stunning. Not a lot of western tourists. I'd recommend an overnight so you can get up early in the morning before everyone gets there. When we were there, it was full of students visiting.

I also recommend the JR pass. We were able to use it on the JR system around Tokyo and so didn't have to buy many subway tickets.

You don't need a guide.

Any suggestions for favorite guidebooks?

Tsk tsk.

Ouch! Mea Culpa!

Wikitravel's sections on Japan are really, really good, and largely written by Japanese-fluent locals who know the different towns much better than the usual hack authors living off comps.

That was nice of you......

Thanks, I'm making notes. I did order a JR rail pass which should arrive this week via FedEx.

Go to bookstore. Exclude Lonely Planet, not for any special reason, just on general principles. Then pick another guidebook by which one has the latest copyright date.

I am jumping in as we will also be first-timers to Japan next July

I see plenty of nice hotels (SPG, HH, IC, Hyatt...) in Tokyo, Osaka, and some other big cities.
However, according to tripadvisor, it seems somehow difficult to find adequate lodging in "smaller" cities (i.e. Nara or Nikko, Hiroshima).

How to be sure to make the right choice at the right price (We are not on a budget trip)
Is it better to use Tokyo or Osaka as a "hub" and take the Shinkansen for day trips ?