Im flat footed, had shin splints my entire life, but on cycle it can more intense. Ive gotten used to it, it should fade each day (a little at a time) while on cycle if you do cardio everday when it becomes to intense drop it down speed down to a walk tell it is bearable. You can also just switch to the elliptical, lower impact cardio helps a lot in this area.

Also a high dose of taurine 1g a day should help significantly