With fredericktownes hired help, my site is showing vastly improved rendering times and I have eradicated many bugs and issues. I'm even close to getting the page to validate properly with w3c.org (those darn FaceBook tags are killing it)! I highly recommend you hire him - 30 minutes or an hour of his billable time can do wonders!
There are still a couple of quirks I am working through. As I said in the title, if I enable 'JS minify settings', the w3tc-generated js file is created and called from <head>, but <head> still has the individual js files as well.