I could not find this referenced in any of the threads about window alignments here, so I am posting it for my future reference and for anyone else who may be interested. According the the Fisher Body Manual, to properly align the windows requires the use of Kent-Moore guides or alignment blocks. I have not been able to find any of these new. I have read they show up on EBay now and then. Thingiverse user grcvisuals created a 3d model of the alignment blocks (red and blue) that are needed to adjust the windows. You can download the files from https://www.thingiverse.com/thing:4576213 and 3d print them or upload them to an online 3d print service such as Sculpteo or i.materialise. Two blue and one red block are needed to align the window. I have not done this as my car is not yet far enough along. Perhaps in a few months (hopefully).