I can't understand why would you possibly remove all references to MapleStory, if it's because of Nexon then this is completely idiotic, the last thing they'd care about is whether a certain website contains references to their trademark, which by the way is completely allowed by law since it's a fair use of the trademark (i.e. the name).
In sources/public/members.php you have double commas which can lead to some errors.
http://i.imgur.com/ahHNhFh.png
Another thing is that you should not repeat yourself, instead make a new function to handle this, and call the function in each header.php file.
http://i.imgur.com/HtSXaNo.png
Another small thing is that you use too many double quotes ("), in excessive use of this, it slows the application down a bit because double quotes is used to tell the parser that there's a variable along with the string while there is none. Also this bothers me for some reason (ocd, sorry).
Nevertheless, great job! :)

