Found her listed on page 152, as you indicated, though incorrectly placed between the USS MORSE and the USS MOSHOLU. However I cannot find the reference that you state, where she was re-named the USS FLORIDA. What volume and page is this on?
I also checked the DICTIONARY OF AMERICAN NAVAL FIGHTING SHIPS, through the entire listings under the letter "M" but the USS MUSCOOTA is definitely not listed. I also checked the same series of volumes under the listings for the USS FLORIDA, but there is no mention of a change of name to the USS MUSCOOTA, or from the USS MUSCOOTA to the USS FLORIDA.
As an aside I note that the volumes of the DANFS include many excellent photographs and other images, though the vast majority of these are post-Civil War images. Some of these are action photos, including vessels involved in mine sweeping activities.