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Thank you for your query at DoctorSpring.com
I have read your query with diligence.
Pain in legs after running may be due to sprained muscles or due to compression of nerves due to tight muscles at hip.If this pain is not there before running then back problem may not be a reason for your complaints.
If you are feeling sore at your chest & neck after manipulation therapy then you should stop physical therapy should get evaluated by having x ray of your chest.In meanwhile you may have a mild analgesic like advil for relief.
Hope this will help you.
Feel free to discuss further,
Regards.