I don't think this really belongs in the USMLE forum.
But to answer your question, everything "counts", it's just that some things count a lot less than others. So your Step 1 will count the most. Then your evaluations and grades in clinical rotations. Then things like research, etc may come into play for some residencies. Way way down the list are things like how you did in the first two years of med school. Which makes sense since many med schools are some variation of P/F for the first two years anyhow. So pure med school GPA won't make a huge difference, as long as you passed everything, but having done well on boards and rotations is going to make or break you, and to some extent how you do in the first two years of med school is either going to set you up, or hinder you for doing well on rotations and preparing for Step 1. Hope that helps.