Ok, in F11, the default input manager is ibus, rather than scim. However, if scim is working for you, that's great, don't worry about ibus at this point.
SJIS, shift JIS is the former MS default encoding method. However, even MS has pretty much turned to UTF-8, as has everyone else.
I have a page that although somewhat dated, goes into much of this. Don't worry about the actual instructions though, it's really written for people who prefer minimalist window managers. These days, in most of the desktop oriented distributions, one just sets it the way you did.
However, the chances are that it's coming out in UTF-8 rather than SJIS.
Locales are settings that enable a system to work with certain languages--the LC_CTYPE variable is part of this. One thing you can do is
locale -a |grep ja_JP
This will probably give back something like ja_JP.EUC-JP, ja_JP. ja_JP-UTF-8 and the like. If ctl+space is doing Japanese then you're fine as far as that goes.
My page is at
(The README for scim has it listed with an outdated url that no longer works.)