Attached are some of the photos from the earlier post.
To install the hard plastic 3D printed gauge blocks, insert the leading edge first onto the ridge in the weather strip channel, then push down on the rear edge (nearest the handle) into the track. Remove in reverse. The smaller top blocks (blue) are aligned outboard and the larger front block (red) is aligned inboard. I don't think exact placement is critical. They should snap in place if installed correctly.
The actual steps outlined in the service manual are pretty clear once you've walked through them so I won't repeat them here, but the overall goal is to get the windows flush to the guides along the front and top edges.
Once the window is aligned, be careful closing the door with the window up before the weather stripping is in place otherwise you may inadvertently contact the blow out clip. IIRC, this gets better once the weather stripping is in place. Even after, you'll want to keep checking this to make sure there isn't any interference. I found that with today's less flexible weather stripping and how tight everything fits, I needed to adjust the top of the window slightly inward after aligning with the gauge blocks as this seemed to help the fitment. This also creates more clearance with the blow-out clip and makes the window tuck under the clip better. Softer weather stripping would probably negate the need for this.
The largest issue I encountered while adjusting was when I would set the window parallel to the top edge, then roll the window down and back up, it would not be parallel anymore. I attribute this to the play in the 40+ year old window regulator mechanism. The last step of tightening the up-travel stops takes care of this so don't worry about it too much before that step.
Good luck and let us know how it works for you.