You may have to retake those two C- pre-req anyway because Med schools may not accept any pre-reqs under a C. If your cGPA And sGPA can both be at 3.5, it might be good enough for DO schools, but may still short for MD schools.
Please come back here with MCAT and final GPAs prior to put in your application to see your chances. Right now we are just talking air, too many ifs.