Well one thing jumps out at me. You upgraded core, but not plugins :) And you sure have a lot of them. Sometimes WP has those DB errors when it's trying to do too much and it's timing out. Looking at those plugins, I would suspect that's happening here.
I would start by taking out plugins that aren't absolutely necessary for the running of the site.
These plugins, while cool, aren't giving you as much a benefit as you might thing:
permalinks-migration-plugin-for-wordpress (you usually don't need this after you've used it)
timthumb-vulnerability-scanner (if you know you're not using TimThumb, you don't need this)
This plugin has been replaced by JetPack, which also has a Twitter tweet-my-post replacement, and a lot of FaceBook replacements.
This plugin isn't needed since you have WordPress SEO, and it does this:
Counter plugins are, generally, just going to slow you down. You really don't need THREE:
Personally I also don't really recommend any 'security' plugin, but you've got a lot more than you need:
I would go through those and remove ... well. All of them, really. But if you want to keep one, pick one. And let it not be Captcha, please. They're really horrific for users.