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According to Stolba's Music in the Life of Thomas Jefferson, his music library contained no works by Mozart. If Jefferson ever heard Mozart's 40th, it may have been Alexander Reinagle that brought it to his attention.
Reinagle was a composer and impresario of musical theater and a personal friend of Mozart's as early as 1764. Drummond's Early German Music in Philadelphia says that Reinagle's group performed symphonic works in the 1780s, including compositions by Mozart. Cripe's Thomas Jefferson and Music says that Jefferson subscribed to a 1792-1793 concert series given by Reinagle's Philadelphia Company, and may have attended the entire series. The Company had a twenty-piece orchestra; nothing comparable could be found farther south. Krauss's Alexander Reinagle, His Family Background and Early Professional Career states that Mozart sonatas were among the works performed. The sample programs I saw didn't show any whole symphonies, though.
Reinagle also composed and published a piece called "The New President's or Jefferson's March". Later, he relocated to Baltimore. According to Cripe, Jefferson was also a patron of a Marine Band in Washington, DC with Italian enlistees as musicians. It played a piece called the "President's March" at Jefferson's inauguration in 1801.