The guide fails to mention that the joystick ribbon cable is locked into the motherboard. You can use a spudger to lift the grey tab, leveraging upwards on the side opposite of the ribbon cable. The tab will pop up and should make getting the ribbon cable out (and back in) easier.
I followed this guide and ripped the ribbon cable while attempting to get it connected back to the system. If I had known the grey tab unlocks, I might not have ripped the cable by trying to force it back under the pins. My iFixit tweezers were also very sharp, and may have cut the ribbon cable. Would anyone be able to recommend something gentler for the ribbon cable?