John Stephenson, the actor who portrayed George Armstrong Custer, is actually much older than the real Custer was at the time the series was set. Stephenson was 42 years old when the series aired. The real Custer was born in 1839, which would put him in his mid-twenties in the 1865-1867 time period, during which F Troop was supposed to be set.
The highest rank Custer would attain after the expiration of his commission as general of volunteers on January 31, 1866 would be Lieutenant Colonel - his rank at the time of his death at Little Big Horn on June 26, 1876. As a brevet general, he could be referred to as, "General" and also wear the rank of general. He just couldn't get paid for it.