Yes, the Zynq device is the XC7Z035-L2FBG676I. It's suspicious that pin B11 shows up as a GND pin in Vivado. Are you seeing similar problems connecting other signals between the AD9361 and the XC7Z035?
The reference design source files are on Github. If you download (or clone) the 2015_R2 repository, you can rebuild the Vivado project using their TCL scripts. Instructions for doing so are on their wiki.
We haven't created a board def file yet, but I'll put it on the list to create in the next week or 2.