Did you notice any headaches from the impact of the jogging at all? I tried some light jogging and I've noticed that after a few minutes, a mild headache comes on.
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The headaches could have a number of causes. Honestly my best assessment is your body IS still healing, it went through major trauma, and your head is reminding you of this.... its worn down, don't wear me down more! I get headaches all the time.. pretty much 24/7, and so I try to identify 'oh this is my normal headache', or 'oh too much exercise', so on so forth.
It COULD be from the trauma associated with repeated micro-fracturing along the scar lines (probably the fear), but I personally kind of doubt that. After this long most of it has reconfigured and now its just a matter of swelling reduction slowly.