I am a double major (in CS and physics) at a top-5 university in both. I was really hoping to do graduate studies in physics and have been keeping up a 3.8 GPA taking 18-19 units per quarter (max is 20). However, my first semester of junior year I began taking serious graduate courses and really overextended myself. Finals week I did not balance take-home finals and studying for actual finals, and ended up with a 3.3 GPA for the quarter. This is pretty bad, considering I took 3 grad courses that awarded solid As to half the class and the other two were core upper-division courses. If I had performed above median in all classes I should have had at least a 3.85 or so. I don't even have an excuse besides taking too many classes at once.
How can I best fix this quarter of poor grades in terms of a grad school application? Assuming decent research experience, will retaking the two classes that I earned 'Bs' in next year be a bad sign for admission committees from top research programs? My overall GPA went from 3.78 to 3.70 after this, and I earned Bs in classes closely related to research work that I would like to pursue. I learned a lot and aced most homework assignments, but really just did not perform well on the finals due to insufficient time to study/write them up.