Shoes for oddly shaped feet
You should look at using mountain style Shimano SPD compatible shoes.  In general, mountain shoes have a little more room and give and there are a lot of brands that are SPD compatible. 

Keen has a line of cycling shoes and sandals that you can find at larger outdoor retailers like REI or many places online.  I mention REI specifically because in the past I have ordered two sizes of clothing and footwear online and returned the one that didn't fit with no hassle. 

My experience with Keen footwear is that the run a little wide all over and are especially wide in the toe box.