Lot of factors can cause foot pain in a marathon runner. There are intrinsic factors like the muscle strength, flexibility etc and extrinsic factors like the shoes, terrain etc.
Next Steps
Try local warmth to the feet for 5 to 10 minutes before you start running & cold application after your run. Scale down the distance to half & gradually ramp up the distance before you look to improve the timing
Health Tips
You can also consider podiatric evaluation of your feet & style of running evaluated by a running coach