Does this school require LORs? Talk to all your LOR writers, tell them your circumstances. If you have medical/personal/even psychiatric issues have someone familiar with you who can attest to how awesome you are write an LOR and mention that. Describe everything, or if the school requires LORs, just have an LOR for everything you want on your resume, it's worth a few GPA points to do that. I know some people with much better GPAs who were rejected from one of my programs, where i was alternate listed. Any sane person would wait-list them over me, and outright reject me, but somehow I beat the odds, I still can't believe I wasn't rejected, since the school wants a 3.0 overall and in pre-reqs, but i had a 2.77 in pre-reqs and a 2.908 overall. I also did not do extremely well on the GRE.