Have been to Japan before, Tokyo and Kyoto. Will be in Japan mid-June:

Arrive Tokyo 4pm, take JR to Hakone

Day 2 Hakone (Hotel Ra Kuun? any other suggestions? mid priced near JR or bus)

Day 3 Takayama (Minshuku Sosuke v. Shimyoshi Ryokan?)

Day 4 Takayama/Shirakawa-go (is this possible?)

Day 5 Nagoya (Gifu cormorants)

Day 6 Osaka (Hilton v. Westin?)

Day 7 Osaka (Nara)

Day 8 Kyoto (staying at Westin Miyako)

Day 9 Kyoto

Day 10 Kyoto

Day 11 Nagasaki (need hotel recommendation)

Day 12 Fukuoka (need hotel recommendation)

Day 13 Fly to Tokyo and home

Is this logistically efficient? Will have 2 week JR pass.

Thanks

Day 3 - I assume you mean Sumiyoshi Ryokan. I've stayed at both Sosuke and Sumiyoshi, but it was May and I didn't notice if either had air conditioning. Both are fairly basic with shared bathroom and futons to sleep on. Dinner was in the minshuku dining room, but the ryokan dinner in the guest room was better. Also, Sumiyoshi is better located for sightseeing. OTOH, Sosuke is across the street from the Green Hotel which has a nice onsen bath, and Sosuke is the better price. I won't stay at either of those places again unless my budget demanded it. I recommend the Best Western instead.

Day 4 - yes, possible, but not sure what you mean. Are you staying overnight in Shirakawago or Takayama? It is possible to visit S-go as a day trip from Takayama, but you could just visit the Hida-no Sato in Takayama.

Day 5 - I take it your plan is to go from Takayama to Gifu, see the cormorants, and then continue on to Nagoya for the night? Gifu castle is a nice visit but ok if you pass it by (it is not easy to get to, it is small and a reproduction with modern stairs, has a great view). Depending on when the cormorant show is over you might be able to make it to Osaka for the night instead of Gifu or Nagoya.

Day 11 - I stayed in two places in Nagasaki. The Holiday Inn is fine and convenient and I would stay there again. It is just off of a main street that has a street car line. Across that street and back a block is a shopping street/arcade. The other place I stayed was at Sakimoto-ya ryokan and I recommend it. It is a very old traditional ryokan in the middle of the main part of the city, nearer to the JR station.

Day 12 - I also stayed in two places in Fukuoka. One was the Hyatt on the Hakata side of Hakata station. Not much in the immediate area, IIRC, but it is an easy walk to the station. The other place was in the Hawks Town area. That area has shopping, entertainment, and restaurants. The place I stayed in was on top of a shopping mall and a short walk to the Hawks Dome where the Fukouka baseball team plays. Catch a game there if you can. I'll see if I can find the name.

Fukuoka airport is easy to get to via a subway.

Your itinerary looks efficient, busy. Better work out exactly how to get to your first night's lodging.

Are you flying from Fukuoka to Tokyo Narita (NRT) or Haneda (HND)?

Thanks. Is Hakone worth it in terms of great scenary? I'm trying to figure out the transportation from Narita to Hakone, will it be easy to get to Hakone if we arrive at 4pm? Alternatively, we could stay somewhere between Tokyo and Hakone for the night. Any recommendations? Yokohama?

Would like to experience the feel of a ryokan, Sumiyoshi's price is reasonable. Reserved room with private bath. Didn't realize there was no air conditioning, will that be an issue in mid-June? Perhaps it would be better to stay there 1 night or stay at the BW. Was planning to stay in Takayama for night 4.

Was planning to visit Hida-no Sato but thought that Shirakawa-go was better since it is a world heritage sight. Is there enough to see in Takayama for 2 days?

Was planning to stay in Nagoya for the night, will consider Osaka instead, but that will be another hour on JR.

No rooms at Fukuoka Hyatt. How's the Nikko? We want a room near the JR since our flight is at 7 am on Day 13 to Narita. Are there trains to the airport early in the morning?

Flight gets in around 8:30 to Narita, our flight home is at 6 pm. Will go to Tokyo for a few hours.

Thanks again.

I haven't been the Hakone so others will correct me, but I think you should skip it and go to:
Day 1 and 2 Kanazawa then the bus
DAY 3 to Shirakawa-go
Day 4 bus to Takayama
Day 5 stay in Gifu (to get your onsen)
Day 6, 7 Osaka (love hotel)
Days 8-10 Kyoto Night train to Nagasaki or Beppu

Of course this is like my trip except I would have liked to go to Nagasaki so I am biased.