The good news is that a lot of grad schools appreciate an upward trend in grades, so you might be ok, but a 3.25 is pretty low.
I wouldn't sat that they're sticklers for 4 years programs. I got in with 27 hours of CC credit, and I've known others that have done the same.
When I applied, I only had one school recalculate my GPA, so it does happen. But it may not be in your favor (as it happened with me).
I don't know if I would explain the GPA, but that may just be me. You seem have some good research/ internship experience. Maybe talk about how those experiences and the important things you did shaped your research interests.
As for what you can do now,y our best bet is probably to gain as much research experience as you can, preferably independent projects that can turn into posters/presentation.