Dear FT'ers, thanks so much for the excellent tips. we'll be in Japan next week for the house hunt, then return home to pack... we'll be a bit late for the school year, but it couldn't be avoided. schedule was just too tight.
Please consider two last questions which I'm sure you've come across -

1. Visas. My spouse is moving within the same employer, a global company. The Japanese office is applying for an intra-company 'transfer' visa and we've been told that the visa can be validated while we're already in Japan.

I have a new employer in Japan, who applied for a 'certificate of eligibility' (CE), and I've been told that once the certificate is ready I need to present it at the Japanese embassy in our home country. So I will probably just wait for the CE to arrive. This is what we did before moving to Tokyo, years ago.
(i'm told that I can also enter Japan before the CE is ready, then take the CE to the nearest Japanese embassy outside Japan, ie. Korea, and get the Visa there. but my guess is this might be a bigger hassle than waiting back home or going back home to get the Visa there).
Any thoughts?

2. My employer is relocating one more person, a US guy, single, first assignment to Japan. The office is at Nagaokakyo, near Kyoto. Where do you think is best for him to live? (Kyoto or Osaka or...? and which areas do you recommend within these cities? )