buy a 2011 or 2012 michelin red guide. using the maps find nearby 1* restaurants. make a list of 5 or so. go to the concierge desk, and have her reserve one for you. have her also write the name in japanese, and numeric location of the place. go out and catch a cab to get you there. show cab the instructions.
huge place. thousands of excellent restaurants. get one close to save cab fare, and time.
do not negelect non-japanese food. i have had some of my best italian and chinese meals in tokyo.
since your internal clock is probably screwed up from the trip over, do lunch as a main meal. much less than dinner.