I had changed my permalink format and after some minor fixing everything seems to be working normally. However, I can't seem to fix one last bug that popped up. I can't even see how they can be related.
I had always had a redirect set up from http://www.myurl.com/admin to http://www.myurl.com/wordpress/wp-admin. After changing my permalinks this now gives me a 404 error. Obviously, typing in the URL by hand still works, but I'm stumped.
Here is what my htaccess file looks like:
RewriteEngine on
RewriteCond %{HTTP_HOST} ^combobreaker.com$ [OR]
RewriteCond %{HTTP_HOST} ^www.combobreaker.com$
RewriteRule ^project "http\:\/\/127\.0\.0\.1\:12001%{REQUEST_URI}" [P,QSA,L]
# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>
# END WordPress
ErrorDocument 404 /index.php?error=404
RewriteCond %{HTTP_HOST} ^combobreaker.com$ [OR]
RewriteCond %{HTTP_HOST} ^www.combobreaker.com$
RewriteRule ^admin$ "http\:\/\/www\.combobreaker\.com\/combobreaker\/wordpress\/wp\-admin" [R=301,L]