Thanks for sharing your evocative essay--it brought back memories of my Tokyo omakase meals. I also watched Jiro Dreams of Sushi and couldn't wait to have an authentic omakase experience in Tokyo. We went to Sukibayashi Jiro Roppongi Hills (helmed by Master Ono's son) and enjoyed ourselves immensely. I believe the original location helmed by the father is no longer open for reservations by foreigners unless you stay at certain luxury hotels (you have to have connections to get in!).
Yet our favorite omakase meal was at Sushi Masuda. I highly recommend it if you return to Tokyo. The sushi bar fits 6 patrons and you feel like you're in an artist's studio, watching him work. It's a truly exceptional sensory experience--a feast for the eyes and the mouth!