While you'll probably need to be willing to take a lower salary then you would get in the US (especially compared to tech hubs like silicon valley), be careful not to emphasize that you're willing to work for a very low salary as part of the application process. Saying this will send a signal that you're a poor developer, and make companies less willing to hire you. Try to keep compensation out of the picture until you've found a company where you're a match otherwise.
Also be aware that Japanese companies typically only hire new grads (they'll make offers during the third year of university) or "mid-career" people (have at least a couple of years experience). Because of this, there are very few entry level positions. There are fewer still that don't require Japanese. While its not impossible to do, you need to be able to demonstrate you have an exceptional aptitude for software development (and having a strong public profile will help get your foot in the door).
Most opportunities for developers are in Tokyo. While its possible to get an opportunity somewhere else, those are few and far between. Assuming it is just you and your wife, and she's going to be working as well, living in Tokyo should be doable.