I hoped to time it for when my eldest son entered middle school, as I think that's the point where most Japanese schools go to shit.
This was a issue for me as well (wanted to ensure my daughter had native English to complement her native Japanese, so we contemplated a temporary move back), but we just decided to bite the bullet and pay for her to get an English education here rather that compromise our lifestyle.
I just decided to apply for Permanent Residency here (fingers crossed!) and am looking to just buy a house in Osaka.
Good luck with both.
Having the red passport helped me out immensely with the latter. PR would have sufficed too I'm sure.