I woke up feeling bad again and went to see the doctor. She gave me a hernia exam (negative) and then gave me a referral to a PT (I couldn't get an appointment until the 31st!). I described my other symptoms but she thought I would be ok and said that I should keep running.
I went home and ate some chocolate before going running. I ran to sugarhouse park and felt a little tight. When I got to the park I noticed that there was such a massive imbalance in my muscles that my right foot wanted to point almost totally out (at right angle to my left). I didn't like what this did to my knee. I focused on rotating the foot back straight (which is how it normally is) and all the pain suddenly went away. For the last 4 miles of my run I felt amazing. I didn't feel sick and my running for was smooth and fast like it was a few months ago. Quite a turnaround.