The lighting isn't too good in this photo, but it shows some of the items I used to clean the windows. During the process of soldering and staining the solder lines I stopped every four or five of hours to clean both windows. I repeated this until I was completely done with the project. So, its safe to say that these windows have been cleaned approximately at least twenty to twenty five times. For the final phase of cleaning, I go into more detail.
I use a large tub to wash the windows in and rinse them with extremely hot water first. To get the Vaseline-like flux and patina stain off of the glass I sprinkle the glass window on both sides with Tide (dry) detergent for clothes. With as hot of water as I can stand, (using plastic gloves to protect your hands) I take a toothbrush and rub the toothbrush on every piece of glass in the design to clean the chemicals off. After several hot water rinses and the windows are dry, I use Hercules wipes (purchased at your local Lockes hardware store) and rub each piece of glass with handi-wipe.
I use Q-tips to get inside and around the edges. The last step is rubbing each piece of glass with these sham/cloth glass towels.