Usual scheme is to position the camplate in neutral.....smallest indent located on the plunger tip. Leave the selector rod grubscrew to the very last. Assemble the selector forks onto the gear clusters, add to the box. Some folks leave the mainshaft until the layshaft is in place, but with the clusters and forks assembled and located on the camplate, push the selector rod through the forks and into the hole in the main case. The tricky part is getting the rod through its locating hole in the inner cover.
If it fouls and you smack the cover down hard, with the grubscrew in place it will break away the thread in the casing. Leave the screw 'til last.
BSA Service Sheets 209 and 311 cover Plunger and S/A Boxes. Two different assembly methods are cited, as regards the order of putting in the gears and shafts. But as both work on either box, use the one that works best for you.
Swarfy.