What could be causing me teeth to ache after a run?

See below: This is one of those problems where a visit to your doctor is necessary to figure out what's going on. Only after a thorough evaluation, including examination and possibly labs and other tests, can your doctor correctly diagnose you and treat you effectively.

Have a hunch...: When i was running and training hard i would both clench my teeth together and breathe through my mouth when i was straining. The vibration from running with my teeth clenched gave me headaches and the cold air mademy teeth ache. Why don't you try wearing a light sports mouthguard like an under-armour or cheaper knock off and see how you do. If it persists, see a dentist to get checked out.

Lots: Exercise increases blood pressure which can cause aching in anything with blood vessels. If all your teeth ache, you may have gingivitis or periodontal disease and you should visit your dentist for an exam to find out for sure.