There's no listing for Noyes in Neil Hurley's
Keepers of Florida Lighthouses or the US Lighthouse Society's database.
However, if he was Collector of Customs that means he also held the position of Superintendent of Lights. That mean that he was responsible for nominating people for any lighthouse keeper vacancies that occurred within his customs area. Assuming Cedar Key didn't have its own Collector yet since the cross-Florida railroad was just being finished around that time, Noyes would have handled appointments for St. Marks Light and maybe Cedar Keys Light. (Egmont Key at Tampa Bay was probably under the Key West Collector; Dog Island and Cape St. George were under Apalachicola. Crooked River and Anclote Keys Lights didn't exist yet.) He would have almost certainly been involved in carrying out orders from the Confederate government to disable St. Marks early in the war too.
Most Collectors in the seceded states kept their duties under the Confederate government.
There are
some postwar records for A. B. Noyes in the collection of the Amelia Island Historical Society in Fernandina Beach.
U of FL has a collection of papers related to Noyes' time as Collector of Customs:
"The bulk of the collection is composed of receipts, vouchers, freight lists, registers, abstracts of duties, accounts, and expenditure lists for the lighthouse and port in St. Marks, Florida. These papers are in nine folders, and are arranged chronologically. The remainder of the collection consists of correspondence addressed to Noyes. The majority of the letters concern receipts of items, duties, and day-to-day business of the lighthouse and port. Other subjects mentioned are smuggling, freight handling, traveling time for ships, and the Union blockade on southern shipping during the Civil War. The bulk of the material dates between 1861 and 1866."