I think you have a relatively strong profile. Your overall GPA might be lower than the top students (e.g. the best profiles published in this forum) but it is still a good GPA. Especially when you say that the physics relevant courses in the later years have a 3.8+ GPA.
As others said, your research experience is also above average and having a publication is excellent.
For the test scores, I think for top tier schools, the average PGRE of accepted students hover around the high 800s (e.g. http://www.pma.caltech.edu/GSR/gre&toefl.html
). So, I would agree with the above person that you would want to get at least the average PGRE score (so 900 is a good goal). Remember that average score means that a good chunk of people (half, if it's the median) got in with lower scores. So, to offset your lower GPA, a stronger PGRE could be useful. But even if you can't score this high, it's not the end of the world.
I also agree that extra-curriculars do not count for much for grad school applications. However, I would still include them because they can make you memorable to the people reading your applications. It might be easier for the committee to remember you as "the applicant that is a varsity footballer" etc.
Overall, you are good enough to be seriously considered at the top schools, so it is well worth the effort to apply to any school that interests you. I would not recommend exclusively applying to top schools though, but I think at the best schools, it's a very stochastic method anyways (so it would be foolish for even the best students to exclusively apply to top tier schools).