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To answer your q, "how will it be viewed by Yale?"
My guess is not very well. Unless you had cancer or one of your parents' died, I don't think that Yale will really care too much about your reasons why you didn't get a high gpa. They have so many qualified applicants w/ high GPAs that it makes little sense to accept a kid lower than than even if there are good "excuses" -- because, ultimately, they are nothing more than excuses. Especially if you don't go to a super competitive high school, you need to be at the top of your class. One B+ is far far from the end of the world, but multiple B's throughout high school isn't good.
That said, I think you have improved your chances by having your counselor explain the causes. You have also improved your chances by taking the hardest courses. You should apply -- and the admissions counselor will give you a fair read. It is impossible to say what they are going to think of it all though.
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