I dug a bit deeper into what the University of Indiana, Bloomington, has to offer. Imagine my surprise when I found an even better program.
Joint PhD in Cognitive Science and Informatics
And hopefully a traineeship with the IGERT group.
For my Cognitive Science education, I want to earn a certificate in Dynamical Systems. For Informatics, I will focus on the Complex Systems track. The IGERT traineeship requires one extra class (plus some classes that I will already take for the PhD) as well as a summer internship. I'm hoping to take that at the Santa Fe Institute, if at all possible.
While I'm still looking into other programs at other universities, I plan on focusing on this one in the meantime.