Frank, there is no synopsis of her service in the pages of the DICTIONARY OF AMERICAN NAVAL FIGHTING SHIPS (none under the name of the Muscoota, anyway), but there is some mention of her service (in the final year of the war), in the pages of the OFFICIAL RECORDS OF THE UNION AND CONFEDERATE NAVIES IN THE WAR OF THE REBELLION. For instance, in volume 17, she is indicated to have been at Hampton Roads, Virginia, and ordered to Key West, Florida, on May 6, 1865. The vessel is also mentioned in several other volumes of this set, and page 152 of volume 1, series 2, includes some statistical data, such as the fact that she was built at New York and delivered to the government on December 7, 1864, and commissioned January 5, 1865, at the New York Navy Yard. Volume 3, Series 1, page 410 indicates that the vessel was originally intended to serve on the Pacific station, in January, 1865, but that she broke down and failed to go. Further details of her service can be gleaned from these references in these volumes. Let me know if you wish for me to check this out further.
Paul Silverstone's volume, WARSHIPS OF THE CIVIL WAR NAVIES includes most of what is already shown in the ORN, Series 2, Volume 1, but no other details of her service in the final months of the Civil War. However, he does include some brief data about her final sale, and later history.