Okay, first off I'm 55 y.o. so most mornings and most times I run I have some aches and occasionally a few pains. For me the trick is to know what is 'normal', what I can ignore (or stretch a bit more) and what is going to blow up if I push it. Most aches I work through, and sometimes they feel better after a short jog, usually by the time I hit my second mile I feel better than I did before I started. If I have PAIN I tend to either take a day off or (more likely) do some cross-training. A couple years ago I ran through (walked most of it) to the end of a race and spent the next three months healing. So when I'm even thinking I might be hurt I try and find something besides piling more work on top of the problem. I have found deep water jogging works really well, the elliptical(which is more convenient) and sometimes the recumbent bike or just walking. However, none of these totally replace running, I think deep water jogging comes the closest.
What would have me concerned is that you are having this problem with so short a distance. My suggestion would be to not move on the any longer runs till you can run at this level without problems. If this means not running the marathon as soon as you would like, better to postpone than hurt yourself. I think most people get hurt by adding too much mileage too fast, including going 26.2 miles in one day when their body is only used to going 15-20 miles in one week. Take your time, the journey is as much part of marathoning as the goal.
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