Henry,
I think your problem isn't the fact that you are training that is hurting you, but the type of training you are doing. Now I don't want to try to sound like your coach, but most milers/5000 types usually do some sort of sharpening training before hitting the track hard (Ex. Fartlick, Long Intervals, Tempo runs.) Judging from you training blogs, you went from slow distance to 5:20 and below running. Yes, you did a lot of hills, but there was no slow migration of running faster. I know you ran a few sub 5:30 mi and a 17:47 5K, but that was off of strength training. How often were you running and 4-5 mi runs or 5X1 mi? Unless I missed something, you didn't.
The problem is you did not let your body condition itself enough you run fast, therefore it hurts you when you want to do so. Your mind in conditioned what your body won't let you do. I don't know what kind of pace you do your daily runs, but it might have or still can help you running some of your miles at a faster pace and maybe shorting your base. If you ease into it, the body will adjust to it better than just going from running slow you running fast. Plus you might even drop a few pounds adding some intensity to your workout.
It seems like you have a strain on the hamstring which isn't that bad. My advise, take care of it, or it will take care of you in a bad way. I don't think now is the time to run 200's. I'm not saying don't run or stop being active, but the hammy needs to heal. Have you considered maybe jumproping, jumping exercises, or even running backwards? I know it sounds silly and crazy, but you need to do something to strengthen it. Not the good news is that you still have time before september rolls around. Maybe just do some long runs, tempo runs, some leg lifting and jumping exercises for the next few weeks. Heal it now. You don't want problems in August.
I understand how important to train and run, but it is just important to take care of yourself. Maybe your body is telling you something. Listen to it. The body is just like a Sports Car. Sometimes you have to take it hard, sometimes you have to take it easy.
We all want you to do well this year and many years to come, but you have to be smart about it.