Short background

I ride a 2013 Cannondale Caad 8 Road Bike.  When I first started riding and soon after I purchased this bike, a friend of mine gave me some SPD mountain bike pedals and cleats.  I went and bought shoes to fit the cleats/pedals and off I went.  That was nearly 2 years and 1000 miles ago.  Recently, after riding about 12 miles or so, my right foot will start hurting on the right side near the ball of my foot.  At first it wasn’t so bad.  I would unclip and let my foot dangle a few minutes and then clip back in and I was good for several miles.  Now, after 12 miles or so even unclipping it doesn’t seem to get any better.  I have to stop the bike, unclip and get off the bike for about ten minutes or so before I can continue.  At first I thought it was the shoes, which it still may be.  But, after sharing the information on some sites I belong too, I’m thinking now that it may be in fact the pedals that I’m using.  Keeping in mind that I’m riding a road bike and using mountain bike shoes, pedals and cleats.

I went to the cycle shop today to speak with one of the salesman and he told me about the same thing.  He also added that the reason that my foot is hurting is that I’ve created a hot spot by using a smaller pedal with a small footprint.  He said that what I need is a pedal with a larger footprint so my weight on the pedal will be more distributed.

For those of you that have way more experience than I do what do you guys think?