Is your job for a US company? If so, you could apply for expedited citizenship for your wife under 319b. (Search forums.) If not, you should have to demonstrate that your job is temporary in nature, and apply for a re-entry permit, although that would only permit your wife to be out of the country for 2 years before she would have to come back to the US and apply for another re-entry permit. If you apply for removal of conditions while living abroad - assuming she is able to maintain her permanent residence in the US, possible, but not easy - it is likely that you're case will be put on overseas hold. (Again, search forums.)
Bottom line, it would be much easier if you waited for your wife to be naturalized before looking for work abroad. If you don't want to wait, you'll have to weigh the hassle of all the re-entry permits and overseas holds and possible loss of her GC with just going and then re-applying for a new GC when you guys decide to come back. Of course, it is rather difficult for the wife of a USC to get a tourist visa to visit the US, but it might be easier for Japanese than for other nationalities, ie Mexicans.
If you can get a job with the US company in Japan that is "engaged in the development of US foreign trade," I think 319b is your best bet. It is mostly used for military service, but there are also possibilities for missionaries and employees of US companies.
Good luck!
T and M got a reaction from Bobby+Umit in Working overseas before eligible to apply for 10 year