You should be rotating your shoes. Ideally, you would have multiple pairs that are different brands/models. Each one would stress your feet in a slightly different manner, allowing you to heal while still being able to run.

Or it could be as simple as your body telling you to lay off and get some rest. Still do your long run each week, but skip some days running mid-week. If you feel like you have to do some cardio, cross train by swimming. I wouldn't bike though or do any other activity that heavily stresses your legs as that would defeat the purpose.

The less I run, the better I feel.  I never run more than 3 days a week.....even in the heat of Marathon Training!  I do 2 days of cross training, so I'm working out 5 days a week.  I never run past 18 or 20 for my longest run anymore (sometimes only 16).  I always run a mile walk 30 seconds - 1 minute to let my body recover (during both training and the actual race).   Also, mentally, it is soooo much easier to only have to "run a mile"!  It may sound lazy, but this is how I get my fastest times and keep injury free. I manage to BQ doing these "lazy" techniques too!  Believe me....I used to be the queen of overtraining injuries!  Don't wanna go there!  Anyways....this is just what I've slowly pieced together for myself after years of waaaayyy too much abuse to my body.  Good luck to you!

I think one of the biggest mistakes i've made (which i'm trying not to anymore) is running my long runs too hard. All I end up doing is wearing myself out. This training cycle, i'm running more than I did last time, but at much different intensities..I'm fresher than last time and don't have nearly the aches and pains.

Using a heart rate monitor on my long runs has helped me keep the intensities down..I have a screen on my garmin that has just my heart rate, no other information. I do my best to keep it in a particular range and let the pace fall where it is, don't even know my pace until my run is done.

I'm also much more aware of using my recovery days as recovery days. I'm not spending 8 hours in the woodshop like I was.