The jig is further used to drill the intake/exhaust hole in the cylinder as this extract from Elmer's instructions describes...
For the ROD, chuck a l/4” rod in the 3-jaw with about 2”
projecting. Drill a center hole with a 3/64” center drill and
bring the tail center up for support. Turn the 1/8” diameter
long enough to cut away the center later. Thread 5-40 with
a tailstock die holder. Use parting cuts to bring to final
dimensions. Hold the l/8” diameter in a small V groove in
the milling vise and mill to 1/8” thickness. Drill and ream
for the Crank Pin. Insert the Piston/Rod assembly in the
Cylinder. Place the drill jig over the Pivot Pin. Run a close-
fitting 3/32” pin through the jig and Crank Pin hole.
Then drill the 1/16” port hole in the Cylinder.