First of all, those grub screws are meant to adjust the suspension arms up and down travel. The grub screws limit the movement of the carbon arms. Not for ride height.
Ride height can be adjusted by adding or removing spacers from the main bulkhead screws, or flipping the spacers around on the kingpin.
If you're running narrow then it should be 5.5 mm measured from the top.
Not sure why the screws are sticking out from the bottom. Maybe check the manual again, there might be something you missed.
That spacer setup is meant for foam tires. I remember Hara running rubber tires and he had a stack of 4 spacers!
http://teamyokomo.blogspot.jp/2013/0...o-yrf-001.html