Hi there,
I know that this original question was posted last month but I wanted to reply (just in case anyone is still checking). We just returned from Japan with our new daughter who is almost two months old and very healthy- we are in love!
We had a wonderful facilitator and things went very smoothly. Our stay in country was 2 weeks long.
It's true that there are VERY few international adoptions from Japan (45 total last year) and that it takes some doing to figure out the paperwork and visa process over there. There are also very few agencies stateside facilitating Japan adoptions. I believe it's also better if at least one parent is of Japanese descent (though I was born and raised in the U.S.).
I just wanted to let you know that, yes adoption from Japan is very much possible. If working with a good agency, the process can be very smooth. I'd be happy to answer any questions.
Best of luck to you!