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Here is the latest on my situation. I have changed themes, restored my site from backup, disabled all of my plugins and I still cannot edit permalinks or widgets. All javascript related functions are still down. What is next?

Delete my site and start over?

I thought this was a theme related problem and tried to change themes but that did not solve the problem.

Since I upgraded to 3.5, I am getting this error message :Missing argument 2 for wpdb::prepare(), wp-content/plugins/wp-super-edit/wp-super-edit.core.class.php on line 114

So far I cannot edit my sidebar widgets or change my permalinks when I am writing a post. I have tried to upgrade WP Super Edit and tried to find a plugin to replace it. Is there a plugin to replace super edit that I can use?