According to the link I posted, yes it is advised to take the majority of your pre-med courses at your 4 year university not at the CC but attending a CC should not hurt you when applying for Medical school.
Taking AP Biology in the summer before 12th grade would be replace the F in your UC GPA, but you still have to report both the F and the repeat grade on your application.
What is your UC GPA if you include the D and F now? Cannot make any judgement until you repeat the course and post your new UC GPA at the end of summer, along with test scores and EC’s. Your Junior year is not finished so a lot can happen between now and then. You are on the right track so continue to do well.