Acquire a TESL or TEFL certificate. There are several ways to do so: online programs, a few days of training at a conference, one or two semester-long certification programs at community colleges or even Master's degree programs in the subject.
Decide where in Japan you want to live. The YMCA has branches all over the country, so there is a good chance you'll be able teach in one of the regions in which you want to live.
Contact individual YMCAs to inquire about available English teaching positions. There is not a single website where English teaching positions are posted for all YMCAs in Japan.
Send a cover letter expressing your interest in open English instructor positions, along with your resume.
Obtain your passport and working visa for Japan.