[miltondts]

"At some point she decided she'd rather stay there permanently."

I don't know anything about you or your relationship, but in my experience that is not how a healthy relationship works. The couple decides together what is best for both. So right there that seems like a huge red flag. Another thing is. Have you talked with her about your difficulties? Finally, it's probably a good idea to talk to a therapist (or a good friend) to get some outside perspective. Hope you get better soon.

Edit: Also, most foreigners share the same experience of moving to Japan.