Do any of the regulator mounting/adjusting bolts move when the glass goes up/down?
Have you checked to see that the bottom edge of the glass is sitting tightly/evenly in the horizontal metal glass channel and that the channel itself is tightly bolted to the regulator arm??
Which model/year Land Cruiser and which door are you working on?
For a US spec FZJ80 with electric windows (front door) the four bolt holes for the motor end of the regulator are not slotted from the factory ie: no adjustment possible. For the short adjuster arm of the regulator assembly that...