Life Decision stuff.. Lived there for 7 years, so if I may add to the pile of opinions:
For you: If you have a chance to go live in Japan - GO. The university sounds like just the thing you'll need to cover yourself without being forced to marry sooner than you planned.
For your lady: Understand that you are being hired into a certain position in order to perform a certain role. If you think there's a glass ceiling in the US, then you're really in for it now. By all means - GO - It'll be the experience of a lifetime. Just remember you're a Gaijin, and don't expect an actual career path. Learn. Cut Your Teeth. Move on when it makes sense. And come back stronger for having done it.
For both of you: Contact the Japanese Embassy sooner, rather than later. Tell them the whole situation. Get their advice and follow it. They can and will help. If you have to leave the country to renew your Vista - It's cheapest to fly to Korea (Shinkansen {bullet train} from Tokyo to Osaka, then a short flight), and when I had to do that drill it took up to 2 weeks.
If you already know a Romance language (Spanish, French, etc...), general usage and word order are basically the same as Japanese. Intonation is basically the same, and so you'll be able to substitute words. Speaking isn't bad... If you want to leearn to read/write.... Well... I hope you enjoy Mind Numbing Memorisation.
Also - Anyone under the age of 30 or so *will* understand simple written English. A small pad and pen are your best tools for getting around in a place where you're suddenly functionally illiterate.