Hi bdh,
Y's is actually one of the shops I try to stay away from. They do have lots of high-end stuff in inventory, which makes them look very flashy, but your experience there seems to be on par with what I usually expect from them. They do stock a lot of stuff, so they are sort of a last resort when I absolutely need something NOW. Otherwise, they do not get my yen. To be fair, I'm sure they do have some decent sales people on staff, and, I have not been to all of their stores.
The shop I mentioned earlier is called Bike & Hike near Komazawa. It's a very small shop, but the owner is a terrific guy and is the mechanic for the Japanese duathlon national team. Not really sure about his fitting capabilities/experience though. They've got some triathletes on staff, including a young kid who had the best Japanese bike split at Hawaii last year (yeah, not much bragging rights there, but...). They will most definitely NOT have your size in stock, but should be able to order from the distributor as long as the distributor has your size in inventory. If the distributor doesn't have your size, then you're SOL. Here's their website. It has a map, but it's not very detailed, so PM me if you need more details.
http://bikehike.jp/ Because real estate is expensive and the logistics providers are efficient, most
prudent bike shops here don't carry much inventory on big ticket items, but are very good about getting stuff promptly from the distributor. The good thing is, you won't have to worry about getting fitted on the wrong bike that just happened to be in stock. These shops won't have the "flash appeal" but if you pick the right ones, they will offer the level of service and attention that the big shops can't offer. And, they'll actually remember you the next time you go back after you buy your bike!
Astroman brought up Westy, which is another great shop, and is one of the few tri-focused shops in Tokyo. The owner Hayama-san has been a fixture in the tri scene for a long time. The shop is on the other side of town from where you are, but perhaps worth a visit. He has his own line of shop branded bikes and is usually very good about customizing to meet your size/needs. A similar shop with tri-focus, but perhaps closer is Omino in Suginami. Again, PM me if you are interested.
Ken