The fuel pump utilizes a rack and pinion to define the pump opening. You've GOT to "essentially" time the relationship of the rack, with the pinion. I used a strong flashlight, to get the rack to start at the proper time, with the pinion. Fiddle with it for a minute or two, and you'll see what I mean (while everything is apart).
I have rebuilt the Indian pumps in the past, and they're not overly difficult to time this critical feature. No dots needed. Just put the rack as close to the "closed " position as you can, while inserting the pinion through the pump body, and meshing with the rack teeth. Of course, the pinion rotation at this point should also correspond with "as close to zero" as possible.
As for the screw that goes into the side of the pump, it's the LAST thing that goes on, AFTER the rack and pinion are timed correctly.