The fact that the trans is shifting properly says volumes to me. The one area you circled looks like a manufacturing defect, which is not in an area that would cause you problems. A rebuild shop could have used anti-seize compound that washed off into that area where the crud was. Again, if it is shifting OK, don't sweat it. Clean the VB up and follow the shift kit instructions to the letter. Take your time and you will have a nice shifting unit when finished.
