As written in the Hyrule Historia, the Link in Spirit Tracks is chronologically the second Link in the Adult Timeline.
Link is originally an apprentice engineer, who becomes a hero by saving the land of New Hyrule from the evil of Malladus. Throughout his adventure, he works together with the spirit of Princess Zelda, who inhabits a Phantom form in certain situations. His appearance is similar to that of the Link from Phantom Hourglass, however, his voice is now similar to that of the younger Link from Ocarina of Time.
Powers and Stats
Tier: High 6-A
Classification: Hylian Swordsman/Engineer
Age: Appears to be about 12
Powers and Abilities: Superhuman Physical Characteristics, Enhanced Senses, Magic, Master swordsman, Expert marksman, Energy Blasts, Elemental Manipulation (Via Whirlwind, Sand Wand, and Bow of Light), Resistance to Soul Manipulation
Lifting Strength: Class 100
Striking Strength: Multi-Continent Class (Capable of breaking Byrne's guard with his sword strikes, can stagger Malladus)
Durability: Multi-Continent level (Survived Malladus' powers exploding out of control and the destruction of the Demon Train)
Stamina: Very high
Range: Extended melee range with sword. Varies from tens of meters to tens of kilometers with ranged weaponry.
Intelligence: Should be no less capable than any of the other Links. Despite being an apprentice engineer at first, Link's combat prowess rose incredibly quickly, and was in the end able to defeat Malladus with some additional help from Zelda.
Weaknesses: Nothing notable