Sorry to hear about your problems Toomchtoodo.
If you were doing good six milers only a few weeks ago, I'd perhaps put your aches & pains down to a virus that your body's fighting. I've had that happen to me.
I reckon, give it a few days or so, like Egglet says, listen to your body, let it fight the bug and then see how you feel about doing a short run, say a three miler.
If it is a virus, Your body needs all it's energy to fight the little b*ggers. Rest is therefore best for a few days and see how it goes.
Hope you feel better soon.
Oh and keep your fluids up.