Planning for physics PhD apps - Classes vs research?
Research experience and track record is more important than courses you have taken.  You will very likely be required to take Jackson E&amp;M for the PhD program.  You might be required to repeat it if you took it before, depending on the program's rules.  Keep in mind that classes you take (or research you perform) after you apply for the PhD program usually do not change your admissions decision.

In sum, I recommend postponing the E&amp;M course.