Hi Dan,
I'm sorry to be the bearer of bad news, but this simply isn't fixable. As you can see in your CheckSUR log, you have a lot of missing registry values and even if I spend hours fixing these, there's a very good chance different errors will appear in their place.
I know this isn't what you wanted to hear, especially as this is a server, but the only way you're going to fix this is by doing a clean install.
Sorry I couldn't have been of more help!
Tom