I'm assuming you meant 54 Pearl Street in Manhattan. There is also a 54 Pearl Street in Brooklyn.
Take the Downtown 4 or 5 trains (of the 4-5-6, the dark green line) from 42nd Street-Grand Central to Bowling Green.
You'll get off at approximately the intersection of Battery Place (east-west) and Broadway (north-south), along Bowling Green Park. Bowling Green Park forms a triangle, with the point facing north, and the Bull statue at the north point.
North is the wrong way for you. You want to go south, on Broadway. If you take the west side of Broadway, it will turn into State Street, but for the purposes of this answer, it doesn't matter. Go south along Bowling Green Park (away from the bull) 1 to 2 blocks to Bridge Street.
Turn left onto Bridge Street, and walk 1 to 2 blocks east on Bridge Street (in the same direction as traffic) to Broad Street. A tiny 1/2 block south of Bridge Street is Pearl Street, and near this intersection is 54 Pearl Street.
Yes- Grand Central Station is the name of the SUBWAY station which is below ground (4, 5, 6, 7 and "s" 42nd St Shuttle lines). The RAILROAD station (MetroNorth Railroad) is known as Grand Central Terminal and is at street level.
VIA subway
Not possible these days. Amtrak no longer has service to Grand Central Terminal. BTW - Grand Central Station is the subway station. The railroad station is Grand Central Terminal.
Grand Central Station & Terminal are located at East 42nd Street between Park and Lexington Avenues. Grand Central Station is the subway station, where you can catch the 4-5-6 (the dark green line, aka the Lexington Avenue Line) or the S shuttle train to Times Square. Grand Central Terminal is the railroad terminal, for trains that are not part of the New York City subway system (like MetroNorth commuter trains).
Grand Central Station
Grand Central Terminal is the name of the railroad station at 42nd St/Park Avenue. Grand Central Station is the name of the subway station which is below Grand Central Terminal.
Take the Downtown 4 or 5 express trains (of the 4-5-6, the dark green line), 3 stops, from 42nd Street-Grand Central Station to Fulton Street (at Broadway).
No, they are two separate subway stations.
No, but it does stop at penn station and you can take the subway
There is no train that runs directly between Penn Station and Grand Central. You have to take the subway: the Uptown 1-2-3(the red line), 1 stop, from 34th Street-Penn Station to 42nd Street-Times Square, then transfer to the S shuttle train (color grey) to 42nd Street-Grand Central.Trains on the New York City subway system operate continuously. There are schedules you can download, but they're often inaccurate.
take the Shuttle or 7 train from Grand Central to Times Square and transfer to the 1 train uptown to 59th Street/Columbus Circle
According to Wikipedia and the MTA themselves, 77 of New York City's subway stations have working bathrooms, and 28 of these stations are in Manhattan. However, according to the Related Link (see below), in Manhattan, only 8 of these stations are actually functioning and open to the public (9 including "the developer-financed wonder bathroom at the Times Square Station"). The only one on the 6 line is the Brooklyn Bridge-City Hall Station. There are also bathrooms at Grand Central Terminal, downstairs, near the food court. The 4-5-6 line stops at 42nd Street-Grand Central Station, but Grand Central Station is the subway station, while Grand Central Terminal is the railroad station. So, you would have to exit the subway system to use the bathroom, and then pay another fare to get back on the subway.