Well how fast are you doing your runs in? Maybe you need to slow down even more then you are now to build your legs back up. You may look into the Couch to 5k program or Hal Higdon has some great programs. I also hear of a lot people doing programs where they run/walk which you may need to do right now.
Good luck on coming back from your injury. Just take it slow and easy and you will be fine.
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