I was fit for shoes at the LBS with my bike at the store.... now (4 years later), riding a trainer with regular pedals and tennis shoes I have no discomfort..
hindsight being 20 - 20, after a few discussions with people it points to this...
http://www.webmd.com/a-to-z-guides/metatarsalgia
I have wide feet and finding bike shoes that are 3 to 4 e and not 200 bucks was a challange 4 years ago.