Is there a way to keep using English as system language on windows 8.1, but have it removed from the language bar?

Solution 1:

it can be removed by moving down english (united states) in language window (control input.dll), and then clicking remove button:

tested on windows 8.1

Solution 2:

I think I solved it, at least in Windows 7 Professional.

On the "keyboards and language" menu go to "Change keyboards" and ask to add a new one in the "Add..." button. Then, go to the language you need (English in your case, because you want English to be the default language) and click on the "+" for "Keyboard", after that select the "Show More..." checkbox and all other languages will be shown. Here you can select your Japanese keyboard layout.

This will accept the input preserving your Japanese keyboard layout, but will keep the defaults (for Office and other software) and menus at English.

Hope it helps!