3-day Tokyo itinerary?

We will have 3 full days in Tokyo. I've listed a bunch of things we want to do (there may be more, but these are the main ones). I would like to know what would make the most sense to put these into three days -- what sequence, and how to get from one to the other. We will have a 7-day JR pass, but I don't know if that's relevant. If you think a subway pass would help we will buy that. (The first day in Tokyo is on a Monday (arriving Sunday evening), then Friday and Saturday (Kyoto and Nara in between). Back to US on Sunday afternoon. Oh, and I have consulted some maps and feel anxious already!

So, in no particular order:

Shimokitazawa ("an incredibly happening and hip neighborhood.")
Tsujiki fish market
Tokyo Metropolitan Building in Shinjuku at night
Karaoke in the evening (recommedation?)
Akasura then boat ride to Odaiba--cruise on the Shimuda River.
A public bath? (recommendation appreciated)
A tea ceremony (only if price is right and not too commercialized)
Kappabashi for plastic food, kitchen stuff
Senjoji Temple
Ueno Park and Ueno market, the long loud market that runs along the train tracks
Yoyogi park, Meiji Jingu (shrine)
Shinjuku
Harajuku on Saturday, (takeshita street) to see the kids, and
Ura-Harajuku (Harajuku back streets) where you find lots of cool, alternative guys' fashion much of which is music orientated (my son is in a band at home!)
and maybe the Pokemon headquarters? (maybe too young for my son, maybe not!)
I doubt we're interested in the place with all the electronics unless there is extra time. We are also not really museum people, or Imperial Palace people, necessarily. We would rather use any "extra" time getting from site to site just wandering interesting side streets and exploring the little ins and outs of Tokyo.

thank you for your directions

Hopefully you haven't already purchased your 7-day JR Pass. You really won't be getting anyway near your money's worth out of it. You are better off purchasing a Suica + N'EX. It's easy to use and you will be saving a ton of money, unless of course, money is no object. You can use the Suica on the subways also.

http://www.jreast.co.jp/e/suica-nex/index.html

I didn't notice that you will be going to Kyoto.