If the glass rocks at all it means that the forks are not aligned in the Y-plane. If that’s the case, it’s time to get out some “heavy equipment.” Using a length of 2x4, place it between the fork legs so that the short end is behind the leg that needs to come forward near the bottom (the long end is in front of the leg that needs to be pushed back at its lower extreme).
For example: in my case, when I used the glass on my tubes, the glass had a gap and clicked at “A” and “D.” That meant that, when examining the lower end of the fork tubes, the right tube is behind the left tube (from the rider’s viewpoint). So I put the 2x4 behind the right tube and in front of the left tube as is being shown here. The tube with the green arrow is being moved forward in relation to the tube with the blue arrow, which relatively speaking, is being moved backward. Does it matter which moves forward and which moves backward? No, not at all. We really don’t have too much concern with the tube’s relationship with the bottom of the fork yoke- only that the tubes are lined up in the "Y" plane.
I tied the long, protruding end of the 2x4 to the rear frame and using a length of rope (or alternatively, you can use a ratchet strap), I put tension on the fork legs to bend them into alignment. When you get that set up, leave the bike that way for a while. Here’s what the setup looked like:
The rope method is sort of large-scale variation of a traction device they teach in the Boy Scouts (or at least they use to when I was in Scouts). It is referred to as a "Spanish Windlass". The rope goes around the frame and the 2x4 twice, then it is knotted off at the end. Place the handle of the mallet in between the four courses of rope and twist it around a few times until there is sufficient tension on the 2x4, then the handle of the mallet is rested on the valve cover. Don’t get too carried away here. It doesn’t take a whole lot of force to move the tubes in this plane. Just be sure to attach the rope to the frame of the motorcycle and not a car or the wall because you will end up moving the bike about the garage. This method can create a lot of force, so be sure to use a structurally sound piece of lumber here.
You can drill a large hole in the end of the 2x4 to slide onto the fork leg or make "V" cuts to help it grab the tubes to make it a bit more stable when setting up the process. You could also use a chain link fence post wrapped with rags that can be taped in place instead of the 2x4. Don’t be afraid to ask for assistance from someone who can hold the 2x4 in place while you tighten the rope or strap. After about three or four hours, remove the bending assembly and let the forks sit for a few hours. Then, using the glass plate once again, recheck the alignment. Repeat as necessary until you get the tubes into the alignment in the Y-plane. I checked mine after about two hours and found that they had become aligned, and after 24 hours of resting they held their adjustment! Because they were out about .070" to .100 or less (I didn’t measure it), I thought they would take a lot longer to get into alignment. Your results may vary.
In the Clymer manual it shows another procedure to check for alignment in the "Y" plane using two straight edges and then sighting across them by eye. I personally consider that method wholly inappropriate as it will not give the accuracy that the piece of plate glass can. It also involves completely removing the fork assembly, an unpleasant task with an RT.