After being excommunicated from the Latter Day Saint church, Goodson decided to return to his work as a musician. In late 1839, Goodson travelled down the
Missouri River to
St. Louis for a New Year's Eve performance at the grand opening of a new hall at 2nd and Market Street. For the performance, Goodson played "
Mozart's La Clemenza di Tito". Upon returning to Far West in early 1840, Goodson and the family moved to
Rockport, Missouri. Goodson and Margaret had four children; Mary Hope (b. 1838), John Edward (b. 1840 d. 1852), Frank Faith (b. 1842 d. 1852), and Lillie(b. unknown). Goodson continued to pursue musical education and performing as a career in
St. Louis while maintaining a residence in Rockport, becoming Professor of Music at Kemper University in
St. Louis. During these years, he and his family travelled the Missouri River a great deal by steamboat. In 1846, Margaret drowned in the Missouri River when the steamboat Radnor sank near
Boonville, Missouri, becoming one of the great tragedies in Goodson's life. The boat would never be recovered. On July 10, 1846, Goodson married his widow's sister, Elizabeth Dawson, and subsequently moved to
Cincinnati, Ohio, where he would continue teaching music. It was in 1850 that he first met
Ralph Waldo Emerson while he was on a tour in
Cincinnati. Emerson wrote of their encounter in his journal. Emerson persuaded Goodson to follow him to Massachusetts, and introduced him to the
Boston Athenæum in late July, 1850. Emerson also mentioned Goodson along with
Alcott and
Hawthorne in notes about forming a "Boston Club". On December 21, 1850, his first performance in Boston, Goodson played two organ fugues by
J. S. Bach, one in F sharp minor and one in E major. On August 15, 1851, Goodson was appointed conductor of the Handel and Haydn Society in Boston, a capacity he served in for a short time. At the concert of January 24, 1852, Goodson played a prelude and five part fugue in C sharp minor by
Bach, probably upon the piano, though the instrument is not stated. He was described by
John S. Dwight in his book History of the Handel and Haydn Society as "an accomplished musician and organist. A thinking man, too, with mind much occupied in philosophical and social questions. We have an impression that he stayed not longer than a year or two in Boston and then sought his fortune in the West." John would remain the conductor of the Handel and Haydn Society for one year and then leave with his family to settle in
Missouri for good, leaving around the time that both of his sons died of smallpox. In early 1852, Goodson established a farm with his family in
Franklin County, Missouri. Goodson and his wife Elizabeth had 7 children together; Thomas Carlyle (b. 1847), Elizabeth Emerson (b. 1849), John Edward (b. 1851), Frank Faith (b. 1854), Henry Clinton (b. 1857), Cora (b. 1859), and Anna Elizabeth (b. 1863). In 1858, Goodson travelled to
St. Louis in order to establish a home for his family and to pursue further employment in the music profession. The
New York Weekly Review had this to say about a performance Goodson gave in
St. Louis on May 8, 1860: "The music-loving people of our city were favored with quite a treat last evening in the shape of an organ exhibition given by Mr. J. E. Goodson, at St. George’s Church." The periodical goes on to say, "Mr. G. certainly did himself great credit as a performer and musician. The program for the occasion contained nothing but the best pieces; among others, two by
Handel, two by
Haydn, three by
Mozart, two by
J. S. Bach, and one by
Mendelssohn, the influence of which cannot fail of having a good tendency. The introductory was from
Handel’s Concerto in D Major, and was played with true artistic skill, as likewise were the others, of which I cannot go into detail. Of the playing of one piece I was particularly pleased; Favorite Air, with Variations, including Adagio on the Cremona, from
Mozart." ==Final years and death==