I closed up the sides of the water ports today. First step was using a wire brush attachment on the Dremel to clean off the dried coolant, then measure and mark the new edge. Then I used blue painters tape along the edge to form pockets, and then gooped in enough JB Weld to fill the pocket. After about 5-6 hours it was firm to the touch, and I pulled away the tape.
After it fully sets up overnight I will put the gasket on it and see how close I got. I went over the line a little bit (you can see the marker in the 2nd pic, it's the black shadow spot right past the seam), so I may use the sanding disc to form a lip, or I may leave it alone. Pretty happy with it so far though.