Fixed! October 28, 2013
The latest update to run the webserver with nohup seems to have fixed my server issues. I did get a server crash soon after changing the script, but I couldn't track it down, but it's been running non-stop for a few days now.
Finally I can put this to rest. Also, out of it, I got more efficient tracking as well as more detailed error messages in some instances, and less detailed error messages in others (for files not found, for instance, it just spits out 'Not found: ' and the file name, instead of a whole stack trace.).