Regarding the index marks on the indicators, I noticed my right one is more accurate if it's reversed. Place the indents on the inside instead of the outside. This is to accomodate the difference in axle size between the solid axle diameter and threaded diameter portion of the axle(they're different) This keeps the adjuster from bending or deforming. (If you remove the chrome adjuster, you'll notice that the hole size is different between the indent side and the non indent side).
The index marks are only a reference point, I measure the axle in the swingarm adjuster grove with round feeler gauges (1/4 inch long sockets) to keep things square.