Trip to Japan

Check out the japanrail.com website and price the shinkansen from Nagoya to Kyoto, round trip and Tokyo to Nagoya RT. Why are you arriving in Nagoya five days before the conference? Can you change that to arrive into Tokyo or Kyoto (Kansai International)?

Himeji and its castle is a day trip from Kyoto; Nikko is a day trip from Tokyo.

In September, Tokyo will have sumo wrestling.

Go to japan-guide.com and start clicking around -- great site for tourists.

If all you want to see are Kyoto and Tokyo, and presumably you want to see one before and the other after your conference, JR Pass won't be a good deal as you need to get a 14-day pass. I suggest you just pay as you go. Nagoya to Kyoto is around 5000 yen on Shinkansen one-way. Nagoya to Tokyo is just over 10000 yen one-way, and you can take the fastest Nozomi which you can't with a pass. As there are several every hour, there's no need to book a seat and every train has several unreserved cars.
JR Pass may become cost effective if you want to make further, longer day trips, say to Himeji and Hiroshima.

If you are just going to Kyoto or Tokyo for a couple days, then back to Nagoya for the conference, the to Tokyo or Kyoto for a few days, then I agree that you don't need a JR Pass.

I suggest cutting out Tokyo. Here are a couple of other ideas:

These are roughly in REVERSE ORDER of recommendations.

Just south of Nagoya is the Ise peninsula which is worth a couple of days and to see Ise Jingu.

Just north of Nagoya is the Kiso Valley where you can walk the Nakasendo and/or visit the towns of Magome and Tsumago. Maybe spend a night in a ryokan.

Nearby to Nagoya is Inuyama with a wonderful restored little castle. Not as magnificent as Himeji, but visiting there and a nearby garden with a small ochaya, and an onsen bath in a nearby hotel, makes for an easy day trip from Nagoya. On the same day, you can visit Gifu. There is a reconstructed little castle perched on top of a mountain with a great view. It takes a ropeway ride and uphill walk to get to.

Further afield from are Matsumoto with an excellent castle, Kamikochi with hiking, small onsen baths, and mountain scenery.

Gero Onsen is just up the Takayama line from Nagoya and is populare with Nagoya-jin. North of there is Takayama, an interesting walkable small city with a few sites.

Shirakawago is a bus ride from Nagoya. This is a World Heritage site and would be a great stop.

You will have a lot of city in visiting Kyoto and Nagoya, so a visit to the village of Shirakawago would be quite a change of scene. I am pretty sure that there are day trips (tour buses) from Nagoya to Shirakawago, but would be better to go on your own and spend the night. Visiting Shirakawago and Takayama or Gero (or both) is easy enough in the time that you have.

My recommendation of Gero Onsen is based on my expectation that you know of, or would research, the proper etiquette for visiting an onsen bath and what to expect.

For Kyoto, I suggest that you look into one of the geisha dances. They are held in April and sometime in the fall, but not sure if it is Sept or Oct. I believe that there is a Kamogawa Odori in Pontocho and/or a Miyako Odori in Gion at that time.

Thanks for your replies - here is our itinerary -
September 10th fly in to Osaka and train to Kyoto
September 11th to 13th Kyoto
September 14th to 18th Nagoya (one of us has a conference to attend the rest are free to tour)
September 19th to 21st Tokyo
September 22nd fly out

1. Would a day trip to Takayama from Nagoya be possible ?
2. Day trip to Hiroshima from Kyoto ?
3. Any other suggestions would be most welcome - Hotel suggestions too.

Thanks

1) yes, it is 2 to 2.5 hours each way by limited express
2) yes, it is about 2 hours each way by Hikari shinkansen
3) see above