You're getting the different throws because of the geometry of the lower to upper surface linkage. Ideally to produce the same throw you'd need the horns to be on the same sides of the surfaces with a hole in one of them to allow the joiner to pass thru and connect to the horn. Does that make sense to you?

It's all due to the angles and rotational arc to linear travel issues. By altering one of the horns to be closer or farther from the hinge line you could slightly minimize the issue but that would require some pretty serious mods. The other option would be to cut off the connector rod horns and re-do your connecting rod so that it attaches to the trailing edges of both surfaces with some arrangement. By having both the anchor points in the exact same spots on the lower and upper surfaces then you would be sure to get identical surface travel motion.