During junior year, should I focus on taking advanced courses in my major for admission to grad school, or can I take courses for my minor?
It sounds like you've got a plan to take all of the courses required for your chemistry core. That being the case, having a physics minor won't hurt you since physics and chemistry are closely related sciences. Having a broader background in a related science will likely help you as long as you have the required core courses. You will also have a chance to do some more upper level chemistry work in your senior year.

Doing research will really stand out in your application as well, and this is at least as good as having done an upper division special topics course. Since graduate school is more focused on research, having undergraduate research experience lines up well with your plans, and that will stand out to the selection committee.  

My one suggestion would be to start looking ahead to where you want to go to grad school. Look at their graduate college page and see what courses are required for applicants and make sure your remaining course work lines up with that. Also look at the faculty research pages and start thinking about who you want to work with as a graduate adviser (a critical decision!). Contact a couple you're interested in and ask for a phone or skype informational interview. In addition, talk to your current research adviser or the principal investigator you're going to be working with this summer. Most likely, they will be very happy to mentor you in preparing for graduate school, and also helping you establish contacts at your schools of interest. My undergraduate research advisor helped me open doors to both graduate school and a prestigious post-grad internship that really boosted my appeal as a grad school candidate. Good luck!