Well, it's great you have it working in a subdirectory, but I'm also redirecting anyone from the root directory (in this case, chipsncheese.com/ ) to a sub-directory (ie. chipsncheese.com/main/ ) which is inherently broken if your code is inconsistent, which it is.
One example would be as such:
sef404.php, line 22
(Which is the improper way to call it btw)
Later down on line 539 however, we have this:
Which is the correct way to call it, via Joomla standards.
You must include the absolute path or else Joomla doesn't recognize the redirected sub-directory structure, not to mention it makes your code actually consistant.
Here's a fixed example of line 22 (note that $GLOBALS isn't required):
Fixing such inconsistencies in both the admin and component files made it possible for your extension to work properly once again.
Chips N Cheese - Custom PHP installs and the like!