rolling scuppers under . . . Scuppers are openings in the sides of the ship that allow water to run off the deck; the Hispaniola's position and motion of the sea are causing it to roll back and forth sideways until the scuppers are under water.
booms spars extending from the masts to hold the bottoms of the sails outstretched.
blocks pulleys or systems of pulleys (in this case, for manipulating the sails).
manufactory factory; manufacturing plant. (The sort of factory Jim may have had in mind, in the eighteenth century, would have been something like a fabric mill, whose heavy looms operated with much noise and shaking.)
backstay a stay (heavy rope or cable used for support) extending aft (toward the rear) from a masthead to the side or stern of a vessel.
the ship [had to be] warped . . . To warp a ship is to move it by hauling on a line fastened to a pile, dock, anchor, and so on; in this case, the lines were fastened to the ship's boats and the ship hauled by its oarsmen.
conned the ship . . . To conn a ship is to direct its movements, specifically by giving directions to the helmsman, who operates the tiller and actually steers the ship.
the man in the chains . . . the crewman using fathoming lines to measure the depth of the water on either side of the ship's bow.
a strong scour with the ebb . . . To scour is to wash or clear as by a swift current of water; here the ebb (outgoing) tide is very strong and has cleared away a channel deeper than it was when the chart was drawn.
grog diluted alcoholic liquor, especially rum.
pikes weapons, formerly used by soldiers, each consisting of a metal spearhead on a long wooden shaft.
we'll fight the ship . . . we'll fight from the ship, using its weaponry.
gaskin a legging or gaiter (a cloth or leather covering for the instep and ankle).
by the stone A stone is a British unit of weight equal to fourteen pounds; hence, Jim is saying Ben Gunn may have all the cheese he wants.
catechism a handbook of questions and answers for teaching the principles of a religion.
chuck farthen on the blessed gravestones Chuck-farthing is a game, usually called "penny-pitch" in the United States, in which small coins are tossed or chucked to bank off a wall or obstacle of some kind, with the player whose coin lands closest to the obstacle winning and taking the others. Ben Gunn is saying his career in vice began with this mild form of gambling, apparently using gravestones in a churchyard as backboards. (Later, in a conversation with Livesey, Silver will use "playing chuck-farthing with my life" to mean gambling with his life.)
clove hitch a kind of knot used to fasten a rope around a pole, spar, or another rope; used figuratively here, it means a tight spot, a very difficult situation from which there seems to be no escape.
Union Jack the national flag of the United Kingdom.
