I used the washers to keep the horizontal window guide arm from separating from the guide track. like your picture shows. Since the amount of separation is different for all, the amount of washers varies.
there are pictures in my gallery showing this detail.
I test the alignment by checking how the glass rests on the mount while it is unbolted in various up/down positions.
the glass should rest on the center of the top of the mount while the mount is snug to the track.
In other words; the glass runs in fixed guides front and rear.
When the mount separates like yours, the track is not aligned, so the glass pulls the mount away from the track.
It is not a problem with the track guides!