Thanks for your response!
At the time of applying I had three publications... two first author and one second author (also from an undergraduate mentee) as well as some scholarships from my university... Also finished my MSc and have been working for the last two years in my field and had some relevant non-peer reviewed publications from this experience as well.
I am anxious to get the rankings back because I just don't know what I am doing wrong...I think there are just too many awesome candidates out there!?