I have been doing much research on John C. Blacker, as well as the other forty-one stowaways from Melbourne, and have come to a dead end in relation to Blacker, after he left the cruiser. All I have so far, is the following, as transcribed from my database:

John C. Blacker (surname also shown as Blackar), born about 1829; stated to be an Irishman; was a captain in the English merchant service; had previously commanded the merchant vessels White Swan and Saxonia; also commanded the merchant vessels, Pirate (to Otago, in June, 1861), Hydra (to Otago, in February, 1862) and Blue Jacket (to Liverpool, in June, 1862); joined the CSS Shenandoah as captain’s clerk; placed under arrest, June 25, 1865, for fighting with master’s mate Cornelius Hunt; one of the signatories who petitioned lieutenant Waddell, in September, 1865, to steer for Cape Town, South Africa, at the end of the cruise of the CSS Shenandoah. [Temple 974; ORN 1, 3, 782; Argus (Melbourne) newspaper, dated Tuesday, November 29, 1864; CSS Shenandoah Deck Log; Whittle 169; merchant shipping data also obtained from the Victorian Public Records Office web sites titled “Outward Passengers to Interstate, UK, NZ and Foreign Ports 1852 – 1876” and “Unassisted Immigration to Victoria” at http://proarchives.imagineering.com.au/index_search_results.asp.]

We do know that Blacker's servant, Duke Simmons, also followed him aboard the SHENANDOAH, and Simmons was the only non-white who enlisted from Melbourne. As far as I know, Blacker did not publish any memoirs. Although we are aware that he was an experienced mariner for the India, China and Australian seas, I cannot find any evidence that he returned to, or settled in Australia, so I assume that he may have remained back in the United Kingdom, after the end of the cruise, in November, 1865. A fellow researcher indicated that there was a John Cuddington Blacker who was born in the United Kingdom about the same year (1829/30), but I have not been able to confirm if this is the same person.
From the journal of surgeon Charles E. Lining, a copy of which I recently received from the Museum of the Confederacy, it would seem that Blacker was constantly at loggerheads with several of the junior officers of the SHENANDOAH. At a much later stage I intend to check sources in the United Kingdom for any further mention of Blacker, after November, 1865. Being as experienced as he was, he would have almost certainly returned to a seafaring career.