I've lived in Japan for 11 years now, and have the complete opposite experience from you. While older houses (30~10 years ago) were horribly insulated, houses now are sturdily built, with good insulation (mine has fiberglass and spray-foam composite) and are pretty well put together. If you buy a cheap house, then yeah, you'll have a cheap house -- but that's anywhere in the world.
> If this doesn't sound crazy enough, there are a lot of carbon monoxide related deaths every winter in Japan because many people (especially elderly people) use an ancient heating system called /kotatsu/, where they burn coal under a small table that's covered with a blanket.
Umm.. Kotatsu do not produce Carbon Monoxide. They're usually electric, and you're the first foreigner I've ever seen who has complained about them. (I love them, my wife hates them because once inside, I never leave)
Carbon monoxide poisoning usually comes from eldery in older house where they use kerosene heaters (touyu) for heating. Almost all kerosene heaters have a 3-hour timer though, so it is a little safer than you make out.