exercise intolerance

[a.k.a]

I run about five and half miles twice a week. Clearly, I

[CCF-Neuro-M.D.-SH]

First of all, keep in mind that I am unable to diagnose you because I am unable to examine you, this forum is for educational purposes.    
   The symptoms that you describe are non-specific, but sound the most like normal fatigue.  I suspect that your diet may not allow for adequate glycogen stores in your muscles, you are relatively dehydrated or you have gained some weight and have increased work of running.  Some metabolic diseases and myopathies have very mild symptoms, so I would recommend some testing to evaluate for these.  First I would recommend serum lactate and pyruvate levels along with ammonia to evaluate for mitochondrial disorders.  I would also suggest serum and urine amino acids along with urine organic acids.  I would also suggest an MRI of your lumbar spine to evalute for spinal stenosis. If the above si negative, then an EMG of the lower extremities may be warranted.
I hope this has been helpful.

[problemmatic]

I am not a doctor but the "second wind" phenomenon sounds like descriptions I have read of one of the metabolic myopthies of muscle/mitochondrial disorders.  You might want to look those up and see if anything rings true.

[johnflox]

Have you taken statins (for cholesterolemia)? Have you gone abroad and taken antimalarials (lariam)? Have you taken cipro, levaquin, avelox or similar antibiotics during the last three years?
All those prescription drugs and many others cause ALL the symptoms that you mention when the reaction is rated as mild. In more severe cases, CPK's, aldolase, bilirrubin and other liver enzymes are also elevated.

Just to rule out potential causes, so that you can center your search.