We did this cruise on the Statendam all the way from Hong Kong to Vancouver last year. it is possible to get private tours in any of the ports you mentioned. We were well satisfied with the ship sponsored ones however. I might do private tours in Japan, but would be somewhat reluctant to do so in China.
The two day overnight tour for Beijing, and the Great Wall was marvelous. HAL chose the tour vendors with care. The tour guides were well informed, the buses were comfortable and reliable, and there was no fear of mechanical trouble resulting in being left behind. Not a pleasant thought at all!
The Peace Park and Atomic Bomb Museum at Nagasaki are great. we did that on a tour, then in the afternoon we just walked in the upscale area above the waterfront and had lunch and sake in a world class sushi joint.
You might want to consider doing the fish market in Busan on your own. It is really something to see!
We did not go to Kobe, we did Osaka, Kyoto, Nara instead which was wonderful.
Landlocked in Denver, but cruisin every chance we get.
Polynesia, Carib. '86
Cr. Odyssey, Scandinavia, '91, 30 Day S Pac. 2002
Crystal Harm, Aust., N.Z., '94
Royal Odyssey, AK,'96
Old Cr. Pr. Canal, '97
RCCL, Carib, 1998
Volendam, Car, 2000
Ryndam, 35 day S. Am., Antarctica, '03
Is. Pr., Canal, 2004
Statendam, 34 day China, Japan, AK '06
Cr.Pr., Carib. 08
Eurodam, Atlantic, Med. '10