Looking at my drawings shows that when the bearing bushes for the expansion link are lined up with the holes in the frame, the top of the motion bracket should be flush with the top of the frames. Looks like something is not quite right somewhere. Either the alignment holes are not in the right place (should be 1.09375″ from the top of the frames) or the expansion link bushes are in the wrong place on the motion bracket. As you suggest, the idea is to put a length of bar through the holes in the frames and then through the expansion link bushes on the motion brackets.
The position of the expansion link pivot bushes is the critical issue. If they are too high, the radius rod will be angled up relative to it’s correct position, which will affect the valve events. Also, of course, the slide bar mounts will not line up with the slide bars!
John