Thanks for reviving this, Pius Aeneas -- I've been keeping my eye on the forum, but I hesitate to revive threads as a new poster!
I too am applying to PhD programs this cycle. I finished undergrad in 2014 (UChicago) and did a terminal MA in philology at UGA (excellent program!), which I finished in 2016. OP, like you I had couple shaky years in undergrad -- my mother died, and my grades hovered in the B range for a while. I applied to MA programs on a whim my senior year, and UGA accepted and funded me. I regained my love of the field (and academia as a whole) at UGA, and I beefed up my Greek tremendously (been taking Latin since freshman year of high school, so that's been fine, generally). Partially to lower my stress levels and partially to figure myself out, I decided to take a few years off after I finished my MA and am now in my second year as a Latin teacher at an independent school. I presented at CAMWS last year, and my abstract was accepted for the upcoming annual meeting, so I haven't totally lost touch with academia! My mother was a humanities professor, and I've always wanted to pursue research and undergraduate teaching, so I feel like I'm finally back on the right track.
OP, if you are truly concerned about your GPA/general qualifications for these programs, I highly recommend pursuing a terminal MA to strengthen your application for future doctoral work. There are funded programs available, and it was a spectacular way for me to redeem myself academically. I second Pius Aeneas: your letter writers can do some rhetorical gymnastics for you, and your statement of purpose/writing sample can clarify these issues and reassure the admissions committees that you are driven and resilient.
I have applied to a good mix of Ivies and top 25 schools; broadly, I am focused on the ancient novel (particularly Apuleius, whom I've thought about more than perhaps is healthy), and I have secondary research interests in Greek tragedy and the classical tradition. I'm applying to 13 (!) places total, which seems a bit excessive; I've been "out of the field," so to speak, for a few years now, though, so I'm playing the numbers game. Plus, I have been receiving fantastic advice from my letter writers and mentors, so it was hard to narrow down my choices. We'll see what sticks! My first deadline was today (Duke), and I've submitted the majority of my applications over the past couple of weeks. I am on target to submit the final three this weekend. Fingers crossed for everyone!