I don't know if this may help, but below is my scheme for labeling the various companies of the 6th Ks Cav in the comprehensive roster I'm working on.

Co’A’(#1): Original Co. under CPT W.C. Ransom. Inf. Home Guards. M/O Mar 62.
Co’A’(#2): The 2nd company of this designation. Transferred from 4th Ks Rgt(Co’E’) Mar 62. M/O late 1864.
New Co’A’: Last Co. of this designation. Formed in 1865.
Co’B’(#1): Original Co. under CPT W.T. Campbell. Inf Home Guards. M/O Mar 62.
Co’B’(#2): The 2nd Company of this designation. Transferred from 5th Ks Rgt(Co’D’) Mar 62. M/O late 1864.
Co’C’(#1): Original Co. under CPT Gower. Inf Home Guards. Dec 61 transferred to 4th Ks Rgt as Co’D’. M/O Mar 62.
Co’C’(#2): Formerly Co’E’(#1) under CPT Greeno.
Co’D’(#1): CPT L.R. Jewell/CPT Rodgers. Bulk of Co. appears to have been reincarnated as Co’K’.
Co’D’(#2): Formerly Co’F’(#1) under CPT Orahood.
Co’E’(#1): CPT Greeno.
Co’E’(#2): Formerly Co’G’(#1) under CPT Dobyns.
Co’F’(#1): CPT Orahood.
Co’F’(#2): Formerly Co’I’(#1) under CPT Clarke.
Co’G’(#1): CPT A.W.J. Brown. In Dec 61 transferred to 8th Ks Rgt where eventually became Co’F’.
Co’G’(#2): CPT Lucas.
Co’H’(#1); CPT Dobyns.
Co’H’(#2): CPT Mefford.
Co’I’(#1): CPT Clarke.
Co’I’(#2): Formerly Co’K’/3rd Ks Rgt under CPT VanSickle. Transferred to 6th in Mar 62. M/O Jul 62.
Co’I’(#3); M/I 1863 under CPT J.T. Blake
Co’K’: CPT Rodgers.
Co’L’: CPT H.P. Ledger.
Co’M’: CPT J.W. Duff.