Digging around for info on Spruce Creek I found this postcard of what I believe are the west portals...
In Triumph IV, David Messer relates that the number of tracks through these tunnels kept changing. There was only one two track tunnel here in 1949. By 1900 a second bore had been completed. While both tunnels could accommodate double tracks, Messer states that the fourth track was never completed. This image dates from around 1915 and shows four tracks. Go figure. Apparently the track on the far right is temporary. Don't know for sure. After a cave-in in 1947 the westbound main was moved to the center of the tunnel. This three track arrangement lasted until the 1960's. By then there were only two, one in each tunnel. In the mid 1990's Conrail abandoned the eastbound tunnel altogether. The westbound bore was widened and double tracked. I won't even get into traffic flow. It's even more befuddling.
Hopefully Norfolk Southern left things alone and avoided further confusion for future railfans.
