I want to go to Tokyo.. but don't think I could fit it into this trip - it's pretty expensive from what I have read.
I would choose Tokyo and omit Hong Kong from the list.
Tokyo has the same bustling atmosphere as Hong Kong but it's a lot more hygienic. There really is nothing spectacular about Hong Kong and I'd say from my limited knowledge in this area that shopping would be better in Tokyo than in Hong Kong.
The people of Tokyo are great. They help out foreigners with pleasure. They also have fascinating customs and it's a good experience to dine in a traditional Japanese way.
But yes, Tokyo is more expensive than a trip to Hong Kong in general 
I've wanted to go to Hong Kong for ages so i'll kept it on the list (and I want to take the train up east China, continually stopping at all the villages and such) - I was actually planning on taking a train up to Shanghai and then MAYBE a ferry across to Japan - but this proved to be too expensive.
What I have also thought about is.. flying from Shanghai to Tokyo and then go onto Beijing and continuing my trip.. anyway, I can work this out when the dates come closer..
anyway.. i'll probablly just leave Japan out all together and visit it later in life when I can actually enjoy it a lot more and spend a great amount of time there.