Welcome to SDN! I'm glad you found us before submitting your application.
There are a few things you need to understand about the med school admissions process. First, they are looking for someone who is going to be a successful STUDENT--so while everything matters, at the end of the day the academic metrics (GPA & MCAT) are the most important parts of your application as they give the best approximation of how you will perform in medical school. No matter how nice and caring of a person you may be, it makes no sense to give a spot to someone who either cannot handle the academic rigor of medical school or pass other high-stakes standardized tests (i.e. after the MCAT there is the USMLE steps 1-3, then your board exams for your specialty). If either one of these numbers is below a certain metric, you won't be considered.
The second thing to realize is that this ultimately a numbers game. Each year there are ~50k applicants for only about ~20k seats in US MD schools. There are already more qualified candidates than seats. While certainly some people will have weak points in their applications that can be counterbalanced by strong points in other areas, there is no need for medical schools to "take a chance" on someone with a glaring deficiency.
All of this for saying that you need to get out of the way of the oncoming train. You are overcommitted between being a student athlete, doing research, doing clinical work, and also trying to maintain (or frankly bring up) your GPA and studying for the MCAT. Your diagnostic tests are telling you exactly when you think is happening--you are not retaining the material, and if you take the exam when you're not prepared you're going to get a bad score. I actually think you will have a highly competitive application down the road if you can clear off your other commitments and focus on the MCAT, because pulling a 3.5+ while being a student athlete and checking all the other boxes AND getting a publication is a remarkable achievement! Take the time down the road to really prepare for the MCAT, either next year where you remove some of your other commitments like being an athlete or research, or in a true dedicated gap year. Med school isn't going anywhere, and you want to make your first application as strong as possible.