About permanent resident visa while studying abroad in another country and about spouse of resident

Hi, I am now living in Japan and since I wanted to live in Japan for the rest of my life, I am planning to request for permanent resident visa after working for around 3 years from now. I also planned to study in the US after 3-4 years and comeback to work in Japan after complete the Ph.D.. The question I wanted to ask is

1. If I am studying abroad for 5 years in the US, can I maintain the permanent resident visa in Japan? If yes, then what do I need to do to keep this permanent resident visa.
2. If my spouse (which is not Japanese) is living with me in Japan while I am in Japan. After I go to the US, is she still be able to live in Japan?

The situation is very complicate. We are now holding student visa in Japan, I will be change to working in this year, while she is completing her study in 2 years. After she complete her degree, she planned to working as freelance and it is hard to obtain working visa as a freelance, therefore she may stays in Japan as my spouse. I am curious about the future after I am going to the US. I am also would like to know is it possible for her to change the status of resident from student to spouse of resident.