Excellent points. Within just a couple days I received an interview invitation for the 787 program (possibly Japan related) and looked into attending Keio and Waseda for intensive language programs (student visa). There's Japanese career fair in my area this May with aerospace suppliers (among other industries). There seem to be a myriad of options on the table. I think that if I exercise enough patience and as Glenski mentioned, give her some room to breathe, then I think things will turn out fairly well.
Taking a 3 month 'vacation' does not seem like a good choice, since she would not have much time for me, besides morning and night. She didn't even get the day off before and after Christmas (corporate finance reality). I think that sticking it out with Boeing, perhaps transferring to one of it's partners (Fuji, Kawasaki, Mitsubishi, etc) would not be a bad move either. It's been less than two months since I came back from Japan and I'm sure there's quite a bit that can happen in the remainder of 2008.
For the sake of thinking way ahead. If two people have good incomes, it makes life a lot easier down the road, whether it's for kids, traveling, etc. If my girlfriend wants to pursue a career, that's fine, but eventually the family role will be just as important.
Kyoto Returnee, I like your story, seems like you've had your fair share of ordeals. Australia to Japan is a short flight so that's a plus.