In order for the front suspension to work optimally, the fork tube axes must be (1) coplanar and (2) parallel. If either of these requirements is not met, the front suspension may suffer from stiction/binding.
There are several resources on the web that will help you perform this procedure:
This is a simplified diagram of the upper portion of the front fork assembly. The red box represents the frame steering tube and bearings, which are dimensionally fixed. The dashed blue lines represent the fork tubes passing through the lower triple-clamp and the headlight ears.
Click the diagram for a full-size image.
The following are a variety of factors that can push the fork tubes aligned in Stage 1 out of alignment while assembling the upper portion of the fork assembly.
The fork tubes extend above the lower triple-clamp, and the ends of the fork tubes are flush with the bottom surface of the top plate. In an ideal world, (1) each of the top and bottom surfaces of the top plate would be perfectly flat, and (2) the top and bottom surfaces of the top plate would be parallel to each other. Unfortunately, most top plates are probably bent or warped to one degree or another, which tends to disturb the alignment of the fork tubes. Other than switching to an aftermarket machined top triple-clamp, I'm not sure what can be done about this other than trying to tweak the top plate to be as flat as possible, or fabricating a top plate from a piece of ground tooling plate.
A perfectly flat top plate can be distorted by installing handlebar clamps and handlebars. For example, if one handlebar clamp is taller than the other, tightening the clamps will tend to make the top plate on the shorter handlebar clamp side flex upwards, or the top plate on the taller handlebar clamp side flex downwards. A bent handlebar will do the same thing. On the plus side, two matched handlebar clamps and a straight handlebar will tend to flatten out a warped top plate.
As described above, the fork tubes extend above the lower triple-clamp and the ends of the fork tubes are flush with the bottom surface of the top plate. The length of the headlight ears and the thickness of the headlight ear rubber rings determine how much each tube extends above the lower triple-clamp.
If one or both of the headlight ears + rings are too long, the bottom surface of the top plate will be spaced apart from the bottom nut, and when the top nut is tightened, the center portion of the top plate will flex downwards, thereby causing fork tube misalignment. It may be possible to insert a shim between the bottom nut and the top plate to fill a gap between the bottom surface of the top plate and the bottom nut..
If both of the headlight ears + rings are a little too short, the top plate will not be distorted. Of course this requires the foresight to trim the length of the headlight ears before painting/powdercoating.
Tightening the bolts that attach the headlight shell to the headlight ears can plate a lateral load on the fork tubes if the headlight ear bolts are tightened before the top plate is installed and the tube nuts and top nut are tightened. Consequently, tightening the headlight ear bolts should be one of the last steps of assembling the front fork.