I hope you get a reply from someone more knowledgeable.
Brief internet search comes up with a statement that the State Line tunnel (originally one bore, two tracks: trains were perhaps smaller in those days?) was built "around 1840," and, on another site, that the first through train ran in 1841. So it sounds as if the tunnel is as old as regular service: whether there might have been temporary trackage I don't know, but climbing big hills wasn't something railways in 1840 were happy doing: witness the "Portage Railway," with its mix of locomotive and cable haulage, before the Pennsylvania built the line through Horseshoe Curve.