With that type of foot the problems are related to rigidity and lack of shock absorption. You should not be in a motion control shoe. You should be in a neutral shoe with LOADS of cushioning. And definitely keep stretching and get your foot sized. I would also consider buying something like this to help relieve trigger points in the calves to use before stretching.
Living life like there's no tomorrow.
http://gorgebikefitter.com/
2007 Look Dura Ace
2010 Custom Tonic cross with discs, SRAM
2012 Moots YBB 2 x 10 Shimano XTR
2014 Soma B-Side SS