I've suscribed to the thread, and look forward to hearing about your trip!
As for things to do... I really loved riding the Odaiba Sky Wheel at night. You said you don't like heights though, and the wind is really quite loud up there... but if you can get the courage to do it, I'd definitely recommend it.
You get a lovely night view of Tokyo with all the little red flashing lights of the buildings.
Plus, they have completely clear capsules too if you feel really brave! I didn't go on a clear capsule though... I haven't too long busted my fear of heights. :L