Questions regarding PhD in Linguistics or Applied Linguistics at US universities
As an international candidate you need to think about what your scores mean. I think percentile rank, as opposed to GPA or raw percentage is what is important. In the US a 65.9 would be very bad and I would guess that in the US 75% of the students have a GPA of 3.0 or above and 10% have a GPA of 3.6 or above. In many European countries a 59.9 would be a borderline 2:1 and put you in the 50th percentile.

It sounds like you think your Masters work would be in the top 10%. That is very good. With a little help (both in your letter and by your recommendation writers) schools will figure this out.

One solid piece of previous research is really all that is need to get into a PhD program. 40,000 words is huge. You may want to work on shortening it so you can present it as a paper and send it as a writing sample if English is not your first language.