You can leave Japan up to 12 months without any special procedures apart from saying at the immigration that you are going to come back. But you need to pay tax and nenkin until then. If you get the re-entry permit which allows you to stay more than 1 year outside of Japan with or without a job in Japan but if you have a job, you have to pay the tax and nenkin. If you apply for re-entry permit but come back within a year, then you might have to reapply it and can be difficult to get it. I think it is best you do not come back to Japan at all until you finish everything abroad. But I am not sure about visiting Japan as a tourist in that period. For that, you need to consult the immigration.