base href and canonicalLink have extra directory in urls...

The html_header.php of my site says this:

<base href="<?php echo (($request_type == 'SSL') ? HTTPS_SERVER . DIR_WS_HTTPS_CATALOG : HTTP_SERVER . DIR_WS_CATALOG ); ?>" />
<?php if (isset($canonicalLink) && $canonicalLink != '') { ?>
<link rel="canonical" href="<?php echo $canonicalLink; ?>" />
<?php } ?>

Which outputs this into the pages:

<base href="http://opalessenceshop.com/opalessenceshop/" />
<link rel="canonical" href="http://opalessenceshop.com/opalessenceshop/index.php?main_page=shopping_cart" />

Those extra /opalessenceshop/ directories should not be there. the correct urls are

<base href="http://opalessenceshop.com/" />
<link rel="canonical" href="http://opalessenceshop.com/index.php?main_page=shopping_cart" />

I'm not sure exactly how to edit the html_header.php file to correct this... help?

That's because you've edited your /includes/configure.php file and stuffed '/opalessenceshop/' into your DIR_WS_CATALOG when it should just be '/'.

Hmm.. I'm not entirely convinced that that isn't something the installer put in there during the reinstall I did, since I can't see why I would do that... but I changed them in the configure.php files (both of them) and it is still showing up. Do I need to go into the database to change it?

No. It's ONLY taken from the settings in your configure.php file.
And the only reason the installer would put the extra foldername in there is if you told it to, or if the install happened in that folder originally, and maybe later you moved it without changing the file to match the new folder location.

So, your edits probably aren't saving because the file is read-only. You can't save/upload changes to a file that's read-only. Make it writable first.

I had changed the file permissions to 755 but it was still showing up in the view source... so I used SSH to get in and edited the files directly on the server, and it worked! Whew. That was bugging me! Thanks for your help.