For the projections, i just place a dab of glue on the cog cutout (for the projection). A dab on the back of the cutout and the outermost corners.
I let the projections hang over the back of the cog about 1/16" and place the back of cog on the workbench. Pressing the parts of the cog thats around the projection firmly down to allow the projection to self level. (Good enough for me.)
The rod couplers (Cant think of the correct name for these guys…) just need glue on the back and placed. I didn’t have a 3/4" rod for this set, so i just aligned it by sight and feel.
Undoubtedly the best way to get these couplers aligned correctly is to have that rod in place when gluing.