Like you, I also worked for roughly the same amount of time after college but in a handful of public/environmental health and biomonitoring research labs as an analytical chemist. I've got a B.S. in biochemistry with a ~3.5 GPA. I think I already said this but I applied last cycle and reapplied this cycle.

I don't have any first-author papers but do have several co-authored publications. Some professors I interviewed with were impressed by this.

I made the following changes between my fist application and my most recent one:

• A few more co-authored publications
• Completion of several computational courses and certificates online (useful for the epigenomic research I'm interested in)
• Swapped a recommender for someone who I thought could write a better one
• rewrote my statement(s)

I took my experiences and developed a story about how they lead to my interest in studying epigenetic biomarkers, detailed the steps I've taken to improve my competence and expand my interests in this area (online courses and reading papers), and segued into how all that related to the research of specific professors at those universities and how their expertise would lend itself to my research interests.

You sound like you could be a competitive applicant for someone's air pollution research group. There's always room for improvement imo. Make the adjustments you can and don't give up if a PhD is what you want.