3 week jam-packed Japan itinerary

Hi Lesley,
Wow, it sounds like a great trip. I don't think it's possible to cram too much in. (sleep is highly overrated....) And it looks pretty well-- planned to me.
To-from Nikko (an amazing place), be sure and make a stopover at Utsonomiya and go to one of the many modest restaurant around the station who make Gyoza (meat- filled dumplings.) Fabulous taste. You can vegetarian versions as well.
A lot of my active friends like to cook, and if that's you, you'll have a ball at Tokyo's Kappabashi-Dori, where most of the commercial restaurants buy their supplies (public welcome) There is also an amazing knife shop called Tsubaya, the best selection I have every seen anywhere. Whether handmade Damascus steel or ceramic, they have what you want- and a lot that you want but don't know it yet :-)
Tokyo has so many interesting neighborhoods, it's hard to know how to give advice.
For my part, Kyoto has so much more of interest than Osaka, I would stay in Kyoto and just train it to Osaka for what you need. The Shinkansens run so often, and it's a quick journey, less than check-in / checkout. And with the JR pass, no extra cost.
There are a couple of Mt. Koyas. I guess you mean the one up the valley from Wakayama, with the World Heritage site. I've bicycled up and down that valley and never visited the Buddhist shrine there. Up the valley a bit more is Gojo, with the Riverside hotel with its own onsen, and a five minute walk from there an excellent Italian restaurant run by a Japanese fellow with a huge single-malt whiskey selection - surreal.
Hakone is excellent of course. If you want an onsen experience and snow monkeys, Shibu, just outside Nagano, is an excellent choice. If onsen with spectacular views of Mount Fuji (assuming the weather cooperates,) try Moto-Hakone, up the rest of the way from Hakone and on a beautiful (and a bit touristy) lake.
Just a couple of ideas. Hope you have a great trip!

Hello Lesley,

That's one great plan! With some of the best places to visit in Japan. Before we go any further, let me say that a day trip to Naoshima is not to be missed and one of my personal recommendations! I would also recommend staying the night there if possible, as it is an amazing experience to explore the island in the early morning.

Here are some other suggestions.

I see that you plan to visit Kinosaki and Kenryokuen on the same day. This is pretty hard since Kenryokuen is in Kanazawa and it takes a good amount of time to get there. Both Kanazawa and Kinosaki-Onsen are nice places to visit though, just don't do it on the same day.

For day 17-19. Here you've got a couple of great options. One would be to visit Hakone, the area at the base of Fuji is beautiful and well worth exploring. An other option is a day visit to Nikko, which is home to nature and a lot of the mausoleum and surrounding temples are some of the most impressive in Japan. A last option would be to stay in Tokyo and go on a shopping spree!

Hope this helps,
Daniel

PS: Great post frequentJPvisitor, I just saw it after posting mine.

Cheers, Daniel-san!

Thank you both SO much for you helpful contributions! I have built your suggestions into my itinerary and can't wait!
We are BIG foodies, so anything food related (especially great authentic cuisine, or cooking) is right up our alley.

I think for the spare 3 days, we'll go to:
1) Nagano (and visit Shibu for the Gyoza, yummm - thanks frequentJPvisitor!)
2) Kanazawa and visit Kenroku-en (thanks for pointing out this is in a completely different location from Kinosaki, Daneil-san!) and Geisha/Samurai district
3) The Fuji-Q Highland amusement park and Moto-Hakone/five lakes (although I'm seeing that the transit to the theme park isn't covered by the JR Pass..)

Thanks again :) If you think of anything else, let me know! Much appreciated.