Is the .htaccess file still there?

Hi Dan, sorry I didn't answer your question earlier, I had to go out. Fortunately the break gave me an idea, which ended up working! BTW to answer your question, the whole site was sitting there perfect as pie, it just wasn't working. I know it was perfect, because its back up now without any changes. But before it simply wasn't linking to any internal pages!

For the benefit of future solution seekers with a similar problem, I solved the problem, but not without some effort, and not with a reason, either. I'll list the steps so you can follow them if you wish.

I started by DLing my site to my PC. I then: set up a new blog, set up wp-config.php to the correct database values (of the old blog) and ensured permalinks were correct. I changed the new blog directory name to the old one, logged onto wp-admin and got my site presenting again (make sure you clear the browser cache when you change server subdirectory names). BTW the easiest way to swap a blog is to change ORIGINALNAME directory to ORIGINALNAME_BU and NEWBLOG to ORIGINALNAME.

Even though it presented, it still had the no-internal-linking problem! But this is were I solved it, but why is a different matter. All I did was work my way through the general/writing/reading setting, and without any changes the site recovered itself, and is now working without a problem. I changed back to the old blog and it is working fine, too. It seems if I had just done this without all the other stuffing about, it would have solved the problem. But the experience was worthwhile for troubleshooting practice.

Why did my site recover? I don't know, and only care for interest sake. I'm just happy for a win!

Good luck.