Be aware that if you keep flying in and out as a "temporary visitor," you will get harder and harder questions from Japanese immigration over time, as they will come to suspect that you are illegally working in the country. This happened to one friend of mine who was living with his wife in Tokyo while looking for work for nearly a year. The first couple of times he got minimal questioning, but on his third entry he was taken aside and interrogated for a while.

As long as you aren't making money in Japan, you should ultimately have no problems other than occasional delays at the airport.