Painful feet during workouts

The last year or two I have had horrible pain in my feet during my workout at the gym.
Because of a knee injury, I only run on the eliptical machine the other day I decided to try the recumbant bike which immediately sent shocking pain through my feet.
I thought it was ill-fitting shoes, but they even hurt during Yoga (when I am barefoot)-in fact, they might even hurt MORE during yoga.
I am barefoot at home, and wear flip-flops most days of the year (I hate wearing shoes).
The pain starts, usually, along side my arch on the outer-middle portion of the bottom of my foot-both feet.
The pain quickly engulfs the entire bottom of my foot, as it subsides that middle area is the last part to hurt.
It starts as a sore/burning type of pain then turns to a shooting/stabbing pain sometimes it hurts so bad I could swear my shoe is full of blood (of course there is never ANY marks).any ideas?
how do I stop this pain?
Im a tuff girl, but this pain just about breaks me down!