I have spent some time today to go through all the information. I also got the birth certificate of Moses, son of James/Nathan/Nathaniel. It is attached. So, what I think I know.
1 - James Nathaniel Shuttleworth born around 1799 arrived on the Mangles in 1820 from Manchester. In 1826 he went to WA - King Georges Sound. In 1830 he married Mary Muirhead. In 1833 he received his Certificate of Freedom. He next appeared in 1841 sentenced to a year in prison and working on an iron gang in Woolloomooloo. No further confirmed information.
2. James Naimby Shuttleworth was a solicitor born about 1817. In 1843 he married Eliza Smith but there is no record of children. It appears the marriage broke down as James N married Julietta A MF Bond at some date around 1850. They had three children. Alfred S B in 1851, James J in 1853 and Harry W in 1858. He died in 1859.
3. There was a James Shuttleworth who arrived in SA from London in 1840 on the Orleana.In 1866 he spent 3 months in prison for stealing. In 1872 he got 12 months for larceny. At some point, he married Sarah. He died in 1880.
4. Yet another James Shuttleworth was a convict sent to Van Diemans Land. He arrived in 1829 on the Surry. He married Ann Tozer in 1841 and had a son James in 1843. He worked as a miller.
5. In 1852 James Shuttleworth arrived in Victoria as an immigrant on the Margaret Brock. He described himself as a gold seeker. James died in 1872 in Ballarat.
6. Nathan Shuttle was born in 1804 in Bedford Wiltshire. Father was Nathan and Mother Jane Bird. In 1824 he arrived on the Norfolk after a 7-year sentence was passed down. He was described as a 21-year-old ploughman. During this time he used Nathan and Nathaniel for a first name, and Shuttle or Shuttleworth for a surname.
Nathan was assigned to a Mr Hutchins. In 1928 he was in service to Mr Grant in Bathurst. In 1832 he received his certificate of freedom.
In 1836 he sought permission to marry Mary Ann Cooper. It is unclear if this ever took place, and on probability, it didn't happen.
1843 he spent two days in prison in Sydney for drunkenness. In 1849 he spent a month for assault.
It seems likely that he took on the name of James N Shuttleworth around this time. There were previous instances of the Shuttleworth name in 1824 when he was transported, and 1843 when he was arrested for drunkenness.
One theory may be that James Naimby Shuttleworth was a well-known solicitor at this time. His name was constantly in the paper. Perhaps Nathan was trying to trade on the fame of another Shuttleworth.
In 1851 he married Mary Ann Lewis and lived in the Hawkesbury region. Prior to the marriage, Mary Ann had a son Henry Shuttleworth Lewis. The birth record was for Henry S Shuttleworth but there was a reference to him being called Henry Shuttleworth Lewis as well. They had a number of children after that. Mary Ann 1851, Eliza 1854, Sarah 1856, Moses 1859, Fanny 1864. There may have been other children which we have not been able to confirm. Emma in 1861 and Charles James in 1863.
In 1851 he was still using the name Shuttleworth for the children, but Eliza born in 1854, and subsequent children were Shuttle.
A James Shattle died in 1865 in Windsor and this was probably this person. Once again, a different spelling.