Using a large compass or trammel, you can precisely gauge all the distances and transfer them to a large template of whatever material you choose (paper, cardboard, hardboard, plywood, etc.). For each point you need to lay out, you just need at least two reference points and the distance from each reference point to the point you're trying to transfer.
- Place the (center) point of the compass on a reference point on your table and adjust the radius to match the distance to the point you're transferring.
- Lock in the setting, then move the compass to the corresponding reference point on your large sheet of paper and strike an arc.
- Repeat for the second (and optionally third) reference point. The point you're transferring will be at the intersection of the two (or more) arcs.
Repeat the above steps for as many points as you need to transfer.
Note that if you gauge and mark from 3 or more reference points, any error will be apparent because not all the arcs used to transfer that point will intersect at a single point.
There are also various other geometric construction techniques you can use to construct regular or irregular shapes using just a compass and/or straightedge.
Originally I was thinking you needed to cut square holes in the glass, but after rereading your question it sounds like you just want to notch out the corners of a rectangular sheet of glass. That makes creating a template much easier:
- Cut a piece of cardboard, hardboard, or thin plywood several inches wider than the half the distance between the left and right pairs of pegs.
- Using a knife and metal rule or straightedge, mark the positions of the pegs.
- Cut out notches for the pegs.
- Repeat for the other side.
- Securely glue or tape the two slightly overlapping sides together.
- With the template still in place, use a knife and metal straightedge to trim (or mark, if using thicker material) the template to match the outside perimeter (the perhaps slightly out-of-square rectangle that encloses the pegs).
- If the material was too thick to trim with just the knife, remove the template and use a track saw (or a circular saw with a straightedge guide) to finish trimming the template along the knife marks.