Since I had access to a lightbox, I was able to put the pattern underneath the glass pieces and trace them onto the glass directly. I first traced the pattern with a thick black marker. Then I traced the shapes onto the front of the glass with the same pen (you can buy specialty pens for this, but a Sharpie works just as well).
When you have a lot of similar pieces, it helps to number them so you remember where each of them goes. You can see how I did this with the clear squares of glass in the last picture.