So for a large part of today my blog has been down. I have been trying to troubleshoot for a while on my own and have found several suggestions on the web. Amongst them was ensuring that php5 was being called in my .htaccess file and also by including a php.ini file to set the memory limit. I found a couple of posts on some WordPress forums as well all relating to the same things. I also found some posts suggesting I disable all my plug-ins which I did by removing their folders from my plug-ins directory. Still no luck.
I ended up getting frustrated and called my hosting company 1and1.com. After a few minutes on hold I got through to a rep and she started to run me through everything I had already tried. She then went looking in my .htaccess files to verify that I had indeed done what I said. She came back and then asked to put me on hold. After a few minutes she came back on and told me that it was all working again as expected.
I asked her what had changed and she told me that when I connect via sftp (ssh) I need to ensure that I explicitly close my connection. She said that if a connection gets hung up and not properly closed that this error/behavior can happen. I found that to be a bit strange, but my sites are indeed working again, so I will have to watch to see if it happens again.