Jim: I didn't mean to imply that adding the numbers was improper--I generally do the same (albeit in square brackets) and for the same reasons; also because the numbering often serves as a memory aid. Rather, I only meant that in this case the wrong stanza pattern was reflected. Given how the Mordaunt text is presented in her book, it's easy to confuse the pattern, particularly as she indicated no break between stanzas.

For what it's worth, here's the whole song reformatted into proper stanzas, with solo lines flush, chorus lines indented, verses renumbered:

BOSTON HARBOUR

1. From Boston Harbour we set sail,
And the wind it was blowing the devil of a gale.
    Royals free—Royals free.
With a Ring-tail set all abaft the mizzen peak,
To see Britannia a-ploughing up the deep.
    Royals free—Royals free,
    Studding sails aloft, boys, Royals free.

2. And now the wind begins for to blow,
It's in with your Ring-tail quickly oh.
    Royals free—Royals free.
Clew up the to'gallant sails and take 'em in again;
Bear a hand, jolly tar, at the mizzen fore and main.
    Royals free—Royals free,
    Studding sails aloft, boys, Royals free.

3. Now we poor sailors are a-trampin' on the deck,
With the nasty cold rain all a-blowin' down our necks.
    Royals free—Royals free.
Not a dram of grog can the old man afford;
But it's 'Damn your eyes!' at every other word.
    Royals free—Royals free,
    Studding sails aloft, boys, Royals free.

4. Now that old fellow he's both dead and gone,
But he's left to us his one and only son—
    Royals free—Royals free.
And if he don't prove both kind and frank,
So help me Jimmy, we'll make him walk the plank.
    Royals free—Royals free,
    Studding sails aloft, boys, Royals free.

Source: Mordaunt, Elinor. A Ship of Solace. New York: Sturgis & Walton, 1911, page 235f.
[Note: Her name is misspelled "Eleanor" on the cover and title page.]