"San Pedro" is Saint Peter from the New Testament. Christ called him from his fishing nets to become a "fisher of men" (i.e. a disciple of Christ who would help Christ seek other followers) in Matthew 4:18-20:
And Jesus, walking by the sea of Galilee, saw two brethren, Simon called Peter, and Andrew his brother, casting a net into the sea: for they were fishers. And he saith unto them, Follow me, and I will make you fishers of men. And they straightway left their nets, and followed him.
(King James Version).
His profession may be the origin of the Early Christian secret symbol, Ichthys.
This much-discussed paragraph is an allusion to the crucifixion of Christ. Some have suggested that it means Hemingway saw Santiago as a Christ figure. I think it more likely that it is a "mere" allusion, albeit a powerful one, exemplifying the depth of the agony in Santiago's soul. When he sees the two sharks approaching, he knows it is the beginning of the culmination of his struggles.
This could be another example of his respect for an animal he must destroy--or he could be speaking sarcastically, given the unattractive appearance of shovel-nose sharks. This second meaning is the more likely, given that Hemingway describes them as "hateful," "bad smelling, scavengers."
Santiago is referring to a whetstone, a stone used for sharpening knives.
In Hemingway in Cuba, the authors suggest that this passage is based on Hemingway's own battle, in the 1930s, to land a huge tuna, only to have it devoured by sharks.
He was sure the tuna was world-record size. . . . Ernest heard Dos [Passos] shout his congratulations. . . . Ernest grinned and then looked back to his prize. But his joy and triumph dissipated as he saw one, three, five shark fins surface and begin moving in on the tuna. Like wolves they cut off any escape and hit with teeth bared. In the thrashing of blood and foam, the sharks ripped off twenty-five to thirty pounds of meat with each bite.
Over the melee, a new sound arose. 'Rat, tat, tat, tat--rat, tat, tat, tat!' Bill Leeds stood on the bow of his yacht, firing down at the streaking fins below, a Thompson submachine gun in hand. . . .
But there were too many of them, even with the Thompson. The sharks were feeding on their dead brothers as well as on the great tuna. Within minutes, the spotlight showed an ocean of red.
The tuna was finally brought alongside Cook's boat; all that remained was the head, backbone, and tail. The sharks continued to hit what meat was left in the water. Angry, Ernest grabbed his rifle and fired three rounds into the feeding pack. . . .
Using block and tackle, the two Bimini mates hauled what was left abord. The tuna's head would tip the scale at 249 pounds. . . . (pages 49-50).
A wide range of animals both in and out of the sea track down a food source by quartering, veering from side to as the scent of the food diminishes and strengthens until they reach it.
A diagram of quartering in the context of gun dog training can be found here.
A reference to the Gulf Stream. See first Bookmark for page 9.
A spring leaf would be one of the metal layers of a leaf spring, "a composite spring, used especially in automotive suspensions, consisting of several layers of flexible metallic strips joined to act as a single unit" (answers.com).
Guanabacoa is a township in eastern Havana.