The Clues
First, make sail from the isle o’ bone,
And stop fer a spell where revelers met Davy Jones,
Then sail from where Ned saved Nick from the rope,
And drop anchor where the largest be Alacan’s trope.

A word fer what sails wi’out canvas or crew,
Wi’ a wedge fer a rudder, ’cross shoreless sea blue.
That boold as sheers off from lone ship at world’s end,
That meek as finds death from a stick in a hand.

A word fer what warms the blade on the outside
O’ what ye reach fer when warmin’ yer inside,
Wrapped ’round sworded shoulders an’ o’ the same tint
As a mouth’s tasted don’s pear wi’out swallowin’ a bit.

Mind the men on the isle ’bandoned as the name,
Sung just afore each time purity came.
Wi’ ninth of a small beast ye’ll write a cruel law,
Curse the number of red mouths ye’ll open up raw.

Mind the men as boarded hafter pullin’ an’ fillin’.
Mind the days spent eatin’ chew-liquor seeds wi’out killin’.
Mind the souls who drank, roared, flew, swam, and then mourned.
Curse the pounds got for a gray third un’dorned.

Speak words ye’ve learned, ’sekeetiff-like,
Heave ’head toward ’er threshold, a topman’s hike.
Aloft the las’ dry ones they poor Dutchmen took,
P’raps the only ones savin’ pitcher or book.

A rogue’s life be the sum on the t’ings ’e remembers,
Less the t’ings ’e curses (like the culls ’e dismembers).
Go ’zackly as far as yer life’s account takes you,
Once you cross the sea where your crow’s wakes ’as taked you.

Full Anwser and Explanation

First, make a course fer the isle o' bone,
  This clue tells the reader to sail to Key West. The phrase "lave o' bone" means Key West. The original Spanish name for "Key West" was "Cayo Hueso," meaning "Bone Key." "Hueso" was mistranslated into English phonetically as "West."
 
And stop for a spell where revelers met Davy Jones,
  This clue tells the reader to sail to the island of Savona, off the southeastern corner of Hispaniola. The introduction to Chapter 13: Toasts and Declamations recounts how in 1669, off the island of Savona, 270 sailors drowned when—amid riotous drinking and celebrating and firing of guns-a spark fell in the gunpowder and blew up Henry Morgan's ship. Chapter 5: Threats advises the reader in definitions to four different entries ("do you fancy a swim with Davy Jones?," "I'll blast you to Davy Jones," "I'll see you to Davy Jones," "I'll send you to Davy Jones") that Davy Jones means the bottom of the ocean, especially as a graveyard for those who die at sea.
 
Then sail from where Ned saved Nick from the rope,
  This clue tells the reader to sail to Jamaica. Of the 74 different sources excerpted in the Primer and listed in the Introduction, only one features two characters named "Ned" and "Nick." This is the 1976 film "Swashbuckler," the opening sequence of which depicts Ned Lynch (Robert Shaw) sailing into Kingston at the last minute to rescue his comrade Nick Debrett (James Earl Jones) from hanging at an oceanfront gallows.
 
And drop anchor where the largest be Alacan's trope.
  This clue tells the reader to sail to the island of Grand Turk in the Turks & Caicos. Alacan the Turk is a character quoted in Chapter 5: Threats under the entry "I'll have you for my prize." The excerpt reads: "Alacan'll have you fer his prize, or send you to Davey Jones' locker." (Alacan the Turk, Dead Man's Chest 55) "Alacan's trope," therefore is "Turk." Grand Turk is the largest island in the Turks (but not the largest in the Caicos, so the reference is accurate).

If one were to sail to Key West, then to Savona, then to Kingston, then to Grand Turk-in that order (the same order as the four seasons)—the wakes of one's ship would trace a large letter "X" across the Caribbean. The center of that X-that is, where "X marks the spot"-happens to be the island of Tortuga.
 
A word fer what sails wi'out canvas or crew,
Wi' a wedge fer a rudder, 'cross shoreless sea blue.
That boold as sheers off from lone ship at world's end, That meek as finds death from a stick in a hand.
 
These clues give the reader the word "Dove":

The "shoreless sea blue" is the sky. "What sails wi'out canvas or crew 'cross shoreless sea blue" is a bird. The reader knows that the bird being described is a dove for two reasons.

    (1) The entry for "turtle-dove" in Section 16.5: Food explains that the turtle-dove has a wedge for a tail ("Wi' a wedge fer a rudder"). The excerpt itself makes clear that the turtle-dove was so tame that it was hunted and killed in droves by Dampier and his pirate comrades with bare sticks ("That meek as finds death from a stick in a hand"). The reader should suspect that we're just talking about a "dove," and not specifically a "turtle-dove," because the entry itself makes clear that Dampier was probably not describing a "turtle-dove" but perhaps another kind of dove or small bird like a "mourning dove."

(2) The second clue confirms that the bird we're talking about is just a plain "dove." The bird that "sheers off from lone ship at world's end" is Noah's dove, sent out by Noah to find land. The Ark was the only ship in the world after all else was destroyed ("lone ship"). The only time the world can be said to have been at an "end" was when it was obliterated by the flood. (The phrase "world's end" is doubly appropriate because it is, of course, the subtitle for the third Pirates of the Caribbean movie, "Pirates of the Caribbean 3: World's End.")
 
A word fer what warms the blade on the outside
O' what ye reach fer when warmin' yer inside,
Wrapped 'round sworded shoulders an' o' the same tint
As a mouth's tasted don's pear wi'out swallowin' a bit.
  These clues give the reader the word "coat." Chapter 10: Respectful Address advises that the word "blade" means "fighter." "The blade on the outside o' what ye reach fer when warmin' yer inside" is a reference to the only depiction of a pirate on a bottle of liquor-Captain Henry Morgan on every bottle of Cap'n Morgan's spiced rum. "What warms" Henry Morgan on that bottle is his famous red coat. That hint is a bit difficult, but that's why the reader gets other clues... "Sworded shoulders" are shoulders that have been tapped or dubbed with a sword-that is, shoulders that belong to someone who has been knighted. There have been only three knighted pirates in history: Sir Francis Drake, Sir Henry Mainwaring, and Sir Henry Morgan. "Wrapped 'round sworded shoulders," therefore, is another reference to the coat wrapped around Captain Morgan. The reader knows it's a red coat because it's the same "tint" or color as blood. "A mouth's tasted don's pear wi'out swallowin' a bit" is a bloody mouth: the reader learns in Section 16.4: Torture and Punishment that one of the forms of Spanish torture ("don" means "Spaniard," per Section 13.2: Declamations) was the mouth pear, a metal bulb that was inserted into the victim's mouth and expanded by use of a screw and shaft, thus destroying the victim's mouth and lower face.
 
Mind the men on the isle 'bandoned as the name,
Sung just afore each time purity came.
  These clues give the reader the number "15."

The famous pirate song "Fifteen men on the dead man's chest" is actually a reference to fifteen men marooned on an island known as Dead Man's Chest, now one of the British Virgin Islands. These men were as abandoned, therefore, as a chest is by the dead man to whom it belongs (hence, "'bandoned as the name").

A further clue is "Sung just afore each time purity came." The word "purity" appears in the Primer repeatedly, but only in one sense: it is the name of "Purity Pinker," a character in the television show "The Adventures of Long John Silver." The song "Fifteen men on the dead man's chest" was the show's theme song and played at the start of every episode-that is, "afore each time purity," or Purity Pinker, appeared or "came."

The reader knows from Chapter 3: Flourishes that "mind" means "remember." Thus, the reader is being told to "remember" the number 15. This will become important later on.
 
Wi' ninth of a small beast ye'll write a cruel law,

Curse the number of red mouths ye'll open up raw.
  These clues give the reader the number "39."

Section 16.4: Torture and Punishment describes a "cat" or "cat o' nine tails" as a set of nine leather cords used for whipping. One ninth of a cat ("small beast") is therefore a single whip. The "cruel law" is a reference to "Moses' law," also explained in Section 16.4 as consisting of 39 whip-strokes. The "number of red mouths" (or wounds) that one would "open up raw" while implementing Moses' law would accordingly be 39.

Thus, the reader is being told to "curse" the number 39. This again will become important later on.
 
Mind the men as boarded hafter pullin' an' fillin'.
  This clue gives the reader the number "29."

Section 16.1: The Start opens with an anecdote about how 29 desperate pirates spotted a huge Spanish ship, rowed toward it, opened a hole in their own boat's hull so as to swamp it and ruin any chance of retreat, then boarded the Spanish ship and quickly defeated those on board.

The reader knows from Chapter 4: Commands that "pull" means "row"; the word "pull" is therefore a signal that the "men" being talked about were in a boat. The only men who boarded after "pulling" and "filling" were the 29 discussed in Section 16.1
 
Mind the days spent eatin' chew-liquor seeds wi'out killin'.
  This clue gives the reader the number "57."

Chew-liquor seeds" are kernels of corn. The introduction to Section 19.2: The Echo reads: "Buccaneer Lionel Wafer tells how the natives of Darien made a special corn drink by having their old women chew up corn and spit it into a larger corn-water mixture so as to cause it to ferment . . . ."

The introduction to Section 16.5: Food tells of how buccaneers under Captain Swan survived for 57 days in 1686 on boiled corn alone: "In March 1686 Captain Swan and his privateer company determined to sail from Baja California to Guam despite limited rations, steeling themselves to endure the next sixty days on just eight spoonfuls of boiled corn a day. Only after the ship reached Guam with three days of rations left was it discovered that the crew had decided, should stores run out, that they would kill and eat their own leadership . . . ."

Thus, Swan's men spent 57 days eating "chew-liquor seeds" without killing.
 
Mind the souls who drank, roared, flew, swam, and then mourned.
  This clue gives the reader the number "30."

The same introduction to Chapter 13: Toasts and Declamations that recounts how 270 sailors drowned off Savona when, during celebrations, a spark fell in the ship's gunpowder (above), also points out that Henry Morgan was only one of 30 survivors.

The only "souls" in the Primer who drank, roared (with riotous reveling), flew (through the air as a result of the gunpowder explosion), swam (after falling in the water, and saving themselves from drowning), and then mourned (because 270 of their comrades drowned) are these 30 survivors described in Chapter 13.
 
Curse the pounds got for a gray third un'dorned.
  This clue gives the reader the number "75."

The introduction to Chapter 12: Questions recounts how in 1680 men led by Bartholomew Sharp captured a Spanish ship carrying 700 ingots of gray unpolished metal, and how Sharp's men discarded the treasure hoard thinking it was tin-only to discover their blunder when one of them, who had brought home an ingot, sold one-third of it for 75 English pounds. "Un'dorned" means "unpolished" here, and the reader should know from Section 17.3.3.1: Dropped Middle Vowels that "un'dorned" stands in for "unadorned."
 
Speak words ye've learned, 'sekeetiff-like,
  This clue tells the reader to put the two words he's learned-"dove" and "coat"-together. "'Sekeetiff-like" is pirate for "consecutively." The reader knows from Chapter 17: Pronunciation how "consecutive" might come out of a pirate's mouth as "'sekeetiff," and from Section 22.5: Adverbs how pirates add "-like" to adjectives to form adverbs.
 
Heave 'head toward 'er threshold, a topman's hike.
  This line clues the reader that he's in for an uphill climb toward a building's entrance. He knows from Chapter 4: Commands that "heave ahead" means "move ahead" or "keep going" or "onward." "Threshold" tips him off to the building's entrance. He knows from Section 16.2: Company & Crew that a "topman" is a member of the crew who works up in a ship's rigging, such that "a topman's hike" is an upward climb.
 
Aloft the las' dry ones they poor Dutchmen took,
P'raps the only ones savin' pitcher or book.
  These clues tell the reader his upward hike will involve climbing steps.

"Aloft" (defined in Chapter 4: Commands as "up above" or "upward") reinforces the notion of going upward.

The entry for "walk the plank" in Section 16.4: Torture & Punishment advises that "walking the plank" was something fictional pirates did more often than real pirates in history, but that a rare recorded instance of real pirates in 1829 featured pirates from Buenos Aires forcing the Dutch crewman of a Dutch brig to walk the plank to their deaths.

"The las' dry ones they poor Dutchmen took" are steps-in this instance, the last dry steps the Dutch crewmen took in 1829 just before they plunged to their watery deaths. "P'raps the only ones savin' pitcher or book" is another hint, referencing this as perhaps the only instance outside of film or fiction in which anyone actually took steps along a plank on the way to his death.
 
A rogue's life be the sum on the t'ings 'e remembers,
Less the t'ings 'e curses (like the culls 'e dismembers).
  This clue tells the reader that a rogue's life are the things he remembers, or "minds," minus the things he curses.

The things the reader has been told in the clues to remember or "mind" include the 15 men on the dead man's chest, the 29 pirates who sank their own boat, the 30 survivors of the ship explosion at Savona, and the 57 days of corn-eating. The sum of those numbers is 131.

Now for the minus column. The reader has been told to curse the 39 whip-strokes of Moses' law and the 75 pounds obtained for the sale of an ingot of silver (or a total of 114). 131 minus 114 is 17.
 
Go 'zackly as far as yer life's account takes you,
  The reader is told to go exactly as far (when climbing the steps on the upward hike toward a building's threshold, as he has been told earlier) as "yer life's account takes you." His life's account is 131 minus 114, or 17. So the reader knows to climb only 17 steps.

Important note: Though the rest of the answers in this treasure puzzle are step-by-step logical inferences that one can piece together based on information he's been given in the Primer or that is available on the internet, the one exception is this: In order to know that "a rogue's life" and "yer life's account" are the same thing, the reader must acknowledge/understand that he is a rogue himself. That is, only those who have fully accepted the idea of becoming a rogue (as anyone purporting to master the language of swashbucklers and rogues should) can equate the "rogue's life" of summing memories minus regrets with his "yer life's account," such that he knows to climb only that number of steps. Bottom line: only those who think of themselves as "rogues" or pirates can solve the puzzle.
 
Once you cross the sea where your crow's wakes 'as taked you.
  This pulls together the much earlier hints about how the reader's travels across the Caribbean will mark an X that will land him on the right spot-Tortuga. "Crow's wakes" signals the reader to look at the wakes he's left in his travels, without reference to weird convoluted routes to avoid landmasses (that is, as the crow flies). And the word "cross" is a reinforcing hint to look for where the two wakes cross.

This hint is deliberately subtle because Tortuga-which (1) is one of the three or four most notorious pirate havens in history, and (2) is the only pirate haven to merit its own discussion in the Primer (see the introduction to Section 18.4: Malapropism)-is probably a place the reader is already presuming as a good candidate for the treasure's location. But that's fine, because we want this to be difficult, yet give the reader-when the answer is revealed-the sense that the answer was not too far from his grasp to begin with.
 
Dovecote and its significance to piracy are described in Philip Gosse's The History of Piracy:
  "Driven out of Hispaniola, the settlers found a safe retreat in a small rocky island called Tortuga, or Turtle Island, which lies a few miles off the north-west coast of Hispaniola. Here they settled, formed a kind of republic, and built themselves a fort. For a year or two all seems to have gone well with the little colony, until one day a Spanish force from San Domingo swooped down and wiped it out. But the Spaniards did not stay long and after their departure the 'boucaniers' began to drift back again. It was not until a few years later, in 1640, that the true buccaneer came to stay and flourish there on and off for some eighty years. In that year a Frenchman of St. Kitts, Monsieur Levasseur, a Calvinist, a skilled engineer and a very courageous gentleman, got together a company of fifty other Frenchmen of the same faith, and made a surprise attack on Tortuga.

"This was successful and without much trouble the French took possession of the island. The first thing the new governor did was to build a strong fort on a high pinnacle of rock and arm it with cannon. On this stronghold he built himself a house to live in and named it the 'Dove-cote.' The only way of reaching it was to climb up steps cut in the rock and up iron ladders. Scarcely had it been completed when an unsuspecting Spanish squadron appeared in the little harbour to be met by a withering fire from the 'Dove-cote,' which sank several of the ships and drove away the rest.

"Under the wise governorship of M. Levasseur the little settlement prospered."