I used a jigsaw. I got a couple different blades. Coarse and fine. I experimented with fast and slow speeds and more or less orbital. You have to be careful not to get it hot; it will melt. I used the coarser blade. Use the old windows to experiment. After it was cut, I used a random orbital sander to smooth the edges and take a bit off the width. Don't take the paper cover off until you are ready for final install.
I used the bottom edge of the 12"x36" as the bottom of the two pieces. I cut one long piece with both windows on it. You have to figure how wide of an overlap you want. I used the angled front edge to measure the angled cut in the middle of the glass. This cut isn't that critical. The top edge is important. If the window is too wide, it will be too tight, too narrow, too loose. The front angle edge is critical. You want it to match the front of the frame. The front half isn't supposed to move so you want it tight in the frame.
Hold the glass steady and tight. It can jump up and down. Not good, especially when coming to the end of a cut, it can break.