Having two version of PowerCMS is going to be the approach that you want to take. and your folder structure should look like this:
Main Folder - call it "cms"
Sub Folder - call it "cms_en"
Sub Folder - call it "cms_jap"
On your index page, you could just have to links
<a href="cms_en">English</a><a href="cms_jap">Japanese</a>
I would also recommend that you run the installer separately for each cms version unless you are going to be using the same Database.
let me know if you have any questions.