No matter how long if you have been running, sooner or later you will have some aches and pain. I can remember a few years ago, where I would keep running through this and then wind up being injured and not be able to run for a month or two. Not fun.
Now what I do, if I start to feel a pain or an ache, I will go out for one more run. If I am still having pain the next day, I will take a day or two off. If everything feels fine the next, I will continue to run.
This happened to me this week. I went out Sunday morning and did a fast 5 mile run. I was fine all day on Sunday.
Then I woke up Monday and I could not walk without having any pain. However, if I walked fast or practiced a run, I had no pain. I went out for a run on Monday night. I still had pain on Tuesday morning. I took Tuesday and Wednesday off and by tonight as I am writing this, I am feeling fine. I will be able to head back out tomorrow.