You will also need to add BB-BONE-LOGIBONE to the disabled list in uEnv.txt
After this you need to unexport slot 0. add the flowing to setup_device-tree-slow-r01.sh
sh -c "echo -0 /sys/devices/bone_capemgr.9/slots "
Instead of unexporting slot 0 you could also wipe out the eeprom. This will prevent the default overlay from loading on boot. I did that to mine but I cannot for the life of me remember how I did it. I'm going to look around a bit more and see if I can figure it out again. If I do I will post it here.
Also the addressing changed since the demo was made. The drive now uses word based addressing instead of byte based addressing. See jpiat's post from September 7th above. That should be all you need to do.