How to swap windows using JIS keyboard
Is one of the keys on the right side of the keyboard (like ろ or ￥) maybe backtick? 

If not, you can remap some key to backtick with KeyRemap4MacBook. Save a file like this as ~/Library/Application Support/KeyRemap4MacBook/private.xml:

&lt;?xml version="1.0"?&gt;
&lt;root&gt;
  &lt;item&gt;
    &lt;name&gt;test&lt;/name&gt;
    &lt;identifier&gt;test&lt;/identifier&gt;
    &lt;autogen&gt;__KeyToKey__ KeyCode::JIS_UNDERSCORE, KeyCode::BACKQUOTE&lt;/autogen&gt;
    &lt;autogen&gt;__KeyToKey__ KeyCode::JIS_YEN, KeyCode::BACKQUOTE&lt;/autogen&gt;
  &lt;/item&gt;
&lt;/root&gt;


Then open the KeyRemap4MacBook application, press the ReloadXML button, and tick the checkbox for the setting.

The shortcut for moving focus to the next window can also be changed from System Preferences: