Here is the dial indicator in action on the left side of the box.
I would make a couple of comments on using the dial indicator and jig. First, take some 400 grit sandpaper, a rigid sanding block and make a few light passes along the top of the box, its edges and those of the jig too. Second, take a paint brush or use compressed air to blow away any dust from those surfaces which will have contact with each other. Then rub your hand over the surfaces to see if you can feel any imperfections that may need attention. Finally, wipe the surfaces with a clean cloth. This dial indicator setup is very sensitive to any foreign material, IMO. Getting the two surfaces precisely parallel takes a few minutes. I ended up settling for half a thousandth of an inch as being close enough. Once the small C-clamps are tightened, check for parallel again. Then apply a cabinet clamp on each end to really secure the rail to the box. Check for parallel one last time, just to make sure that you haven't moved something.