I've been reading through this and I have to say there are some convincing arguments. Maybe I should have really looked into getting some orthotics rather than going barefoot initially. I have made an appointment with one of the doctors on this website to see if I have caused any long term damage. The internet is a scary thing with some of it's propaganda. Barefoot running is on hold for me till I get this sorted out.
http://www.podiatry-arena.com/podiatry-forum/showthread.php?s=5aac13d6b556fbc7a999ce7d55cc1995&t=43282&page=35
http://www.podiatry-arena.com/podiatry-forum/showthread.php?s=5aac13d6b556fbc7a999ce7d55cc1995&t=43282&page=35