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Post illness nerve damage?

At the end of 2012 until April 2013 I had a number of throat infections and double vision. The double vision went on from October and cleared up on its own in April 2013. Since this time I have tried to get back into running. Prior to 2012 I was fit and healthy, capable of running 5:30 miles for 3 miles. In recent weeks I can barely manage to run 2 miles at 9:30 - 9:45 mins per mile. Also having seen a Physio I have very unresponsive reactions on my knee and Achilles and when the Physio undertook a scratch test on my feet the reactions were inconsistent. During the double vision I had a CT scan (possibly only on the optic areas of the brain); blood tests and back of eye visual tests all of which came back clear. I am wanting to run again but as I explained above I cannot and for three to four days after running I have very very sore legs. Could this be all connected or is my inability to run at present nothing to do with nerve damage following my illness. In hope of any advice as my deterioration in fitness, strength and my lack of leg reactions have left me worried about a more serious progressive degeneration of my nervous system.
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