In the Wikipdia article on Neptune the discovery is described as a mathematical achievement:
Subsequent observations revealed substantial deviations from the tables, leading Bouvard to hypothesize that an unknown body was perturbing the orbit through gravitational interaction. In 1843, John Couch Adams began work on the orbit of Uranus using the data he had. Via Cambridge Observatory director James Challis, he requested extra data from Sir George Airy, the Astronomer Royal, who supplied it in February 1844. Adams continued to work in 1845–46 and produced several different estimates of a new planet. [...] In 1845–46, Urbain Le Verrier, independently of Adams, developed his own calculations [...]. Neptune was discovered within 1° of where Le Verrier had predicted it to be, and about 12° from Adams' prediction.
Q1: Which method did Le Verrier employ to calculate Neptune's position with such accuracy?
Q2: How would it be done with today's tools?
Edit: Springer has the chapter in the answer available for download.
Edit 2: since the work of Le Verrier seems beyond the scope of a stackexchange question, is it possible to explain the general approach?
Quote from the article above:
Jean-Baptiste Biot attempted to explain Le Verrier's methods in six papers in *Journal des Savants (October 1846, pp. 577–596; November 1846, pp. 641–664; December 1846, pp. 750–768; January 1847, pp. 18–35; February 1847, pp. 65–86; March 1847, pp. 182–187). Arrived at the third paper, he writes: “As I progress in the task I have undertaken, the difficulty of the subject seems to increase.”
Chapter 2, "The Discovery of Neptune (1845-1846)," in the biography Le Verrier -- Magnificent and Detestable Astronomer by James Lequeux may give you what you want. If you google on the chapter title, you can find a link that'll download the entire chapter as a pdf.