Pegasus 40 Outer Foot Pain?

I've been running in Peg 40s for about two months now trying to get ready for a marathon in September. The first 100 miles on the shoe felt fine, but recently after my long runs (12-16mi) the outer edge of both feet have been swelling up pretty bad, to the point where I'm limping on my walk to work.

I do understand there's a chance I'm actually suffering from either a Jones fracture or peroneal tendonitis, I was just really hoping some other folks have had similar pains with the Peg 40 so I can spend money on another shoe rather than the doctor.