Hi Kieth,
Its actually using the file /ClientScript/ckeditor-mojoconfig.js
It uses this file because of this Web.config setting
<add key="CKEditor:ConfigPath" value="~/ClientScript/ckeditor-mojoconfig.js" />
so you can override this setting in your user.config to point to your custom file.
You must use the same toolbar names so you should copy the ckeditor-mojoconfig.js as a starting point but you can control what is included in the toolbars.
Hope it helps,
Joe