An easy way to start is with icons. They will be located in system\app\SystemUI.apk and/or system\framework\framework-res.apk\res\drawable-hdpi. The location of the apps themselves are system\app. Use 7zip to open any rom or theme to find those.
I say icons are easy because all you need is 7zip to swap them out. Stuff like fonts, system text needs a bit more done to get to the .xml files. That info should be in the 1st link. Hope this was some help.