Jason, I tried as best as I could to see the 3D by following the directions at the provided link. It did not work very well for me. Though, I have trouble using both eye pieces on a microscope as well. I almost always need to use one eye piece on microscopes. I have looked at the 3D anaglyphs that people create using the red and green lens glasses.
Great idea, but I too am having trouble getting the images to overlap correctly. Maybe it works best at a certain size. Instead of letting it go the full width you could force a certain size. I resized my window and it got a bit closer.