Community College Coursework
If I am planning to transfer to a 4 year institution and I finished all the transfer prereq, however, I still want to take Genetics, Human Anatomy, Physiology, Microbiology, down at a community college, Would that be accepted for UCI med school or do I have to take those classes at UCI since they're consider upper division.
Each medical school is going to have their own policies in regards to what type of coursework they will accept and from where. So I would contact UCI medical school to get their take.
Overall, though most medical schools prefer that you take any of the courses that you want to use towards your medical school requirements e.g. chemistry, biology, organic chemistry, and physics...these should all be taken at a 4 year degree granting college/university. The reason being you have to show that you are academically prepared to handle the rigors of a medical school education and typically the college/university setting is the best way to show this.
Additionally, getting into medical school is already competitive as it is. So you must also put yourself in the shoes of the admissions committee. If I have two students of equal caliber but the only difference is where they took their courses with one at community college and the other at a 4 year college it almost becomes a nonstarter that I will admit the student from the college/university over the student who took his premed classes at community college.
Although some medical schools will accept community college courses, in the long run and to really improve your chances at admission take them at a 4 year college/university.
Particularly in your situation the upper division courses which you recommended are "icing on the cake" so to speak so you could take them at the community college to save yourself money compared to the 4 year college/university. Especially since these courses would go above and beyond the minimal coursework required for entry to medical school.
Lastly in the words of my physician mentor, "It never hurts to see the material more than once."