You would think that the American Chamber of Commerce would be helpful but when I was setting up our KK here (now some 12 years ago), I checked them out and found there was little assistance they could provide that was not readily available by, say, a web search.

Unfortunately, Japan strikes me as a country that isn't very good for special needs children. As this sounds like a factor to you, I would STRONGLY suggest you make sure this situation can be resolved to your satisfaction before taking the relocation. This means taking the time in advance to see if there are providers you can work with and making the arrangements with those providers.

If by "medical research employment opportunities," you are referring to the possibility of finding meaningful professional employment for a spouse or SO, I suspect you again are likely to be disappointed. Japanese are not used to giving professional positions to foreigners. It happens, but not that often.

I don't mean to be negative -- after all I am writing this from a suite in the Park Hyatt Tokyo with (today) a splendid view of Mt Fuji. This is a wonderful place! But for anything out of the ordinrary in the local culture, you better have all your arrangements taken well understood and planned out in advance.