As soon as your bodyfat goes down a notch the pain WILL stop because your body has been forged through tens of thousands of evolution, your body will adapt,when your fat goes down ur total weight is lower therefore less impact when you run, humans ,were born as hunters they had to run. Just keep running, take some time off to recuperate and it will eventually stop. I used to get crazy shin splits as well last year during basketball practise now i don't think i ever get shin splits, also start your training out slowly, be progressive and do some stretching before you run.
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