Inflammatory response to exercise?

Now, before I say anything else, I will be mentioning this to my GP or practice nurse when I see them & I'm not after an online diagnosis, just picking peoples brains!

Obviously I expect some inflammatory response to exercise, but shouldn't it only be in the muscles I've been using? I generally have a slow & steady approach to excercise (some may say lazy!) & it's really only just struck me, after a run earlier in the week, that when I do push myself it makes me feel totally lousy. I'm not talking about completely over doing it, I was fine calling the dog as I ran & felt pleasantly tired, rather than horribly exhausted, once I got home. I'm fine directly after (including a slight improvement in peak flow) but then for the next couple of days I have that all over ache, like when you're going down with the flu, including sore throat & tender sinuses & the lungs playing up, even the muscles I'd expect to hurt have that heavy, flu-like ache, rather than the ""ouch! can tell I've been exercising feel"".

I had a bit of a google but only came up with systemic inflammatory response syndrome, which sounds a thousand times more serious than anything I'm feeling.