I have a few questions regarding admission into a PhD program in Applied Linguistics or Linguistics at US universities. I could not find any other valuable online sources regarding Linguistics for the answers I seek. Let me start with my qualification. I am an international student with a Masters in English Linguistics and Literature with a percentage of 65.9. Although it's the best language university in my country but it is not that famous anywhere else. My grade average was B with no A or C in any of the individual modules. We don't have GPA system for language studies.

This percentage is regarded with high value in my country and I was one of the top four in my class. However, there is no set grading scale used by the examiners in my country and it is very rare, in fact, almost impossible to score above 70% in any language related field. And that is the case for the most perfect performance. 

My Bachelor's scores are mediocre (59.9%). I was disappointed in myself for not being able to get admission into a medical school (marginally) like the rest of my siblings and ending up doing Bachelors in law and English Literature was a major shock for my planned future career (I had been a brilliant student before). I, however, slowly developed interest in Linguistics and did well in Masters.

1. My first question is, as most good Universities require a GPA of 3 or above with successful candidates usually having more than 3.6, what are my chances of admission? How can I go about explaining my situation as the % of students pursuing Linguistics doctorate at US from my country is very low. Are my scores too horrible?
2. My only research was Masters thesis in a literature related field, titled, 'Autobiographical element in Gabriel Garcia Marquez's "One Hundred Years of Solitude"' of almost 40,000 words. Will it hinder my chance for admission into Linguistics?
3. What else can I do to improve my application and up my chances specifically for Linguistics? How should I lay out my SOP? My ultimate preference would be Berkeley, UCLA and MIT. Should I even think about these universities with such scores?

Any help would be highly appreciated.