I don't know how to put what I'm thinking in words, because so many things are going on in my mind just reading this thread...
First of all, I must say as many posters have said here that you are a very good father for wanting to go through all this for the sake to being able to see your son. So many men would have dropped everything and left after hearing anything resembling what your wife had told you. I can't tell what is truly going on in her mind but IMO she's self-centered and foolish. I may be wrong but am under the impression that she's trying to make you suffer to get even (or so she thinks)? She's acting that way out of jealousy (which may be another side of love)? At any rate, I think what she's doing is ruining her relationship with you.
Regarding the alimony she claims she wants, I don't think it's possible considering the circumstances involved in the divorce. (You may have dated other girls, but she did, too.) In Japan, the size of alimony and child support is inclined to be very small, regardless of who is wrong or responsible for the breakup. If there is evidence that the mother had done something that made the husband leave, there is no alimony at all in many cases. Of course, arrangement should be made for child support, though... (although there are many fathers who are deadbeat dads).
As for your permanent resident visa, I think this is easy, too. Also, there is no need for a lawyer to do it for you, so long as you have help in gathering and filling out forms and documents in Japanese. It will take a few months, but the processing should be easy.
Once again, I do admire your willingness to do this for your son. I'm pretty sure that sometime in the future your son will realize how much you did for him, struggling to be able to see him, and love you all the more for that.
My best wishes!
