Help please

Chris
Hi guys! 
So I have a huge crisis on my hands. Let me give you the full story. 
First, my period has always been irregular. I've skipped months entirely before. I have a long cycle, as well. Beginning July 15, I have been sexually active with my boyfriend. We have had sex about once or twice a week since that, give or take a few weeks. For protection, he has always used a condom and pulled out with the condom on, and we always check afterwards. There have been no breaks or slips in our usage. 
My period is about two weeks late. I have taken two pregnancy tests, both resulting negatively. I know that stress and diet change do effect the period so I am thinking it might be that. I've been crazy busy with work, and I've also gone vegan for the past two weeks. I think that could be a reason it's messing with my cycle. 
Today I've got brown discharge, which could be the beginning of a period for me (this is sometimes how they start) or what I am worried about, the potential of it being implantation. Bleeding. What do you guys think?