You can read below as to how to access these sites as well as view pictures of their present condition.
If you do visit these sites please don't take anything!
A lot of these sites are disintegrating because people are taking stones! So don't do it. Also it is not cool to deface these properties as you will see in the Whitcomb pictures.
As to the purpose of the alignment towers, they served to make sure the tunnel stayed true to its course (as the name implies). Originally grooved iron markers were used instead of towers, however in 1866 when Thomas Doane took over as chief engineer he resurveyed the line of the tunnel and constructed the six towers mentioned here. Each tower consisted of a transit scope (a device resembling a telescope), a sloped wooden roof on the top of the stone structure on the bottom (except perhaps the Rowe Neck tower which shows no evidence of a stone structure.) On that roof there was a red and white pole which protruded 25 feet straight up. Inside the tunnel plumb bobs (pointed metal weights attached to string so to create tension drawing the string down perfectly straight) driven into wooden plugs were hung from the roof at intervals along the line sighted from the towers. A light was used at the blasting head and was moved and sighted until it was perfectly straight. Surveyors told the blasting crews which way to orient themselves, either to go up down left or right.. and of course, always forward! The tunnel was given a slight pitch to allow for water drainage (hence why you cant see one portal from the other). It was of high importance to make sure each portal was the same elevation, 779 feet above sea level.
The alignment towers also played a vital role at the Central Shaft. A Dutch engineer named Carl O. Weiderkinch was given the job to ensure the Central Shaft was in line with the tunnels path. He achieved this by creating two masonry piers along the center line (which was determined by aid of the towers) each 25 feet from the shafts lip. At the end of the pier was an iron block with a thin vertical slit used for sighting the lining towers. When the lining was perfect, two piano wires 1/20th of an inch apart were stretched between the slits. Two 15 lb plumb bobs spaced 25 feet apart were hung between these piano wires. Both plumb bobs were hung inside of 8 inch wooden casings terminating at light oil containers or mercury containers to minimize string vibrations. Line oscillations caused as much as a 1/100th inch variation, so many samples were required when the lines reached the grade. Once a reference point was projected down to the bottom of the shaft, workers could line the tunnel in a similiar way to the method at the portals.