I think I'll ask a few local LBS to see if they would be willing to do it.
The reason I need a wheelbuild in the first place is because I asked SEO to do it and I wasn't satisfied with the results.I've had several wheelsets made there and they've all been good.However,they've recently hired a lot of young staff and perhaps one of the more inexperienced of them was let loose on my wheel.
You could try "Bored" located near the crossing of Route20 and Kannana-Dori near Sazazuka-Station. http://www.bored.jp/ It's more a garage than a shop and you might need to bring the wheel parts you want to use, but this is the trusted mechanic of many Tokyo messengers and Keirin riders. He has a reputation for building great wheels.
Was going to mention this but forgot... My guess is that any shop that handles the keirin trade should be able to build a good set of wheels. I've seen the occasional keirin guy in Bee Cycle linked above...
Another shop coming to mind in the east of Tokyo is Myroad in near Suehirocho/Akihabara in the Northeast of Tokyo: http://www.myroad.shop-site.jp/ It is never busy and the owner Kimura-san is always ready to give free advice and tuning. I don't know about his wheel-building skills, but judging from his competence I bet he is good at it. His shop would probably be my favorite road-cycling store in inner Tokyo.
Also there is Punch Cycle in Asakusa, a favorite of the fixed crowd. While Punch-san is mostly busy drilling holes in track forks, he is also a known mechanic for Keirin and Pro riders and good at wheel building. While it might take some time for him to finish the job, going there has the bonus of late store hours making for a good evening ride. Also there is a wonderful collection of vintage Keirin frames in the second floor, talkative riders outside and a small Sake store next door