Yes, the long rod replaces the 2 short rods and the ball between them. Save the ball. It's the same size as the one still in there and the one in the worm. If you ever lose one, now you have a spare. In particular, the one in the worm can fall out when you pull that left cover off without you noticing.
Seal replacement is usually done (and easier) with the rod removed. Extracting the ball and inner rod is easier when the seal is removed. Many times, the bushing under the seal needs replacing too.