That's what I thought you were talking about. The interlock parts (two balls, CL50 and a pin CL49) are trapped in place by the shift rails (CL33, CL34, CL37). So as you remove each side rail, that will free up the ball on that side. Then the pin will come out with the center rail.
To assemble, you smear some heavy grease on the pin, push it into the center rail and install the rail in the top cover, being sure to thread it through the correct fork & spacer (CL39, CL42). No sense inserted the peg (CL44) just yet, as you'll likely need to do it again
Position the rail in neutral (this might be a good time to install the detent, to hold it in neutral during the rest of the assembly).
Then what works for me is to hold the cover up on it's side, and carefully roll the interlock ball down the bore until it drops into place in its counterbore. While still holding the cover sideways (so gravity holds the ball in place), insert the shift rail for that side. Once the rail is past the ball (so the ball can't come out), you can thread the spacer & fork onto the shaft (CL40/43 or CL41/38). Position that rail in neutral as well.
Turn it up on the other side and repeat. The second side is harder, because the ball likely won't drop all the way into its bore (held up by the pin, which was pushed sideways when you installed the other side rail). Hopefully the slight taper on the end of the shaft will push the ball down into the counterbore (which in turn pushes the pin partly through the center rail and the other ball out into the interlock notch in the other side rail.
Insert the pegs into the shift forks, and then test that the interlock is working. With any rail not in neutral, both other rails should refuse to move.