As said jackshaft position doesn't matter, but if you wanted it aligned you need only take the belt etc off and do again, I wouldn't bother.
As said the lining up is a bit crucial as the cap will foul the underside of plenum etc if not right, the scribed line needs to be dead in the centre of the rotor arm, as just one notch(on the skew gear) will make a difference, but you would immdiately find this with bad running.
tabetha