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.
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.
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! :)