Frank,
Morgan's 2nd KY cavalry used a First National, from what I have seen, for much of its career. CS cavalry in the Western Theater was slow to adopt standardized battle flags of a different pattern until late in 1863 and that was only for a different department.
I do not know if the regiment was rebuilt after the debacle of the Ohio Raid of mid-1863 or not and, as such, it might be hard to know what else they used after that.
greg Biggs