No hacks are needed - the clean install is as secure as you can get at this time. Hacks are only for added functionality.
I'm not sure what you want from a steb by step documentation? You know, you are able to change the colors quite easily from the admin controlpanel?
You can switch your smilies to others if you wish. If you download the graphics package from the vBulletin member area it'll be easier than doing them from scratch IMHO, though.
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