A key element of the plan was the raising of 18 low overhead bridges between Selkirk Yard near Albany and Highbridge Facility in the Bronx to have vertical clearances of at least 17.5 feet (5.3 m); this project was estimated to be completed in 1982.

[2]: 5 Prior to the study conducted by the USCG and the NYSDOT, options to ameliorate the issue included a new rail tunnel under the Hudson River, the rehabilitation of the Poughkeepsie Bridge, the use of the North River Tunnels, a cross-harbor rail ferry, the use of low-profile piggyback equipment and the use of the Harlem, New Haven, and Hudson Divisions through the removal of clearance restrictions.

The Zig Zag Route would have made improvements to the existing Port Morris Branch, including the installation of crossovers, the raising of bridges in some locations, and the depression of the track in others.

This route would have required the construction of a rail trestle with steep grades to avoid conflicts with structures such as the Major Deegan Expressway.

The Shore Route would have consisted of a one-track concrete trestle running from Highbridge Yard to Lincoln Avenue for 1.7 miles (2.7 km).

This option would have eliminated 20 parking spaces at Yankee Stadium, would have restricted the use of a portion of the Bronx shoreline, and would have disrupted some nearby businesses.

This option was estimated to cost $45.5 million, and would have required Congressional deauthorization of a portion of the Harlem River channel, which could have taken at least 18 months to complete.

This option was expected to be cheaper than the Shore Route as its engineering and construction were simpler and because the cost of required real estate acquisitions was much lower.

A new main line track would have been constructed along the southern perimeter of the TOFC yard for trains to and from Oak Point and Long Island.

[2]: 33–34 The line, constructed and owned by the State of New York, opened in 1998 to allow better freight rail access to the city by eliminating the need to use the Port Morris Branch, a more circuitous route that crossed busy commuter lines and whose tight turns (at Mott Haven and Melrose) limited the length of freight cars.

The access was mandated by the Surface Transportation Board to give competition to CSX's post-Conrail breakup monopoly on New York City and encourage freight in the area to use rail.