There is a defect in the Japanese keyboard layout definition, since it misses a definition for the `Win' key. Quite bizarrely, Linux has separate definition files for when the keyboard is used in a console (I think in /usr/share/kbd/keymaps/) and for X/Xorg (/etc/X11/xkb/symbols/).
Helpful hints to create custom keyboard layouts are Creating custom keyboard layouts for X11 using xkb and An unreliable guide to xkb configuration.
First, as root, change to the /etc/X11/xkb/symbols directory. Copy jp to jp_win. Edit jp_win by adding the lines...
key <MENU> { [ Menu ] };
You will also need to modify /etc/X11/xkb/rules/xorg.lst. Under the `layout' section, add the line `jp_win Japanese (win)' below the `jp Japanese' line.
You also need to modify /etc/X11/xkb/rules/xorg. Under `* jp =jp' add the line `* jp_win = jp_win'
You can now choose the jp_win layout from the KDE's control centre (Regional and Accessability -- Keyboard layout).
This now leaves the problem that the left Window key generates F15 from the Japanese (jp_win) layout, but generates Super_L from the en_US layout. I also needed to modify the us layout for my Honeywell keyboard anyway, because it has its backslash|bar key to the left of the backspace key, rather than below the backspace key. I copied the /etc/X11/xkb/symbols/pc/pc file to pc.original and proceeded to edit the `pc' file. There may be a more elegant way to fix this problem without modifying the `original' file...
Add the line...
Change the line in the ``pc104'' section (I have no idea where pc104 is referenced to from en_US)...