I found some interesting information on manning within the Regulars at the beginning of the war in the OR the other night. On page 22 of Series III, Volume 1 is an abstract of returns by arm of service from December 31, 1860. While Robert M. Utley (Frontiersmen in Blue) briefly discussed absenteeism in Regular units on the frontier before the war, to see actual statistics really brought the point home.
The returns for the cavalry included all five mounted regiments and those working at the general recruiting depots. The returns list 82 officers and 3,123 enlisted men present, for an aggregate of 3,205. Even setting aside anyone who might have been stationed at one of the depots or schools, the regiments are badly shorthanded. Quick division renders the numbers to 16 officers and 624 enlisted men per regiment, and one officer and 62 enlisted men per company. The same returns list 100 officers and 482 enlisted men as absent, for an aggregate of 582. This breaks down to 20 officers and 96 enlisted men per regiment, and two officers and nine enlisted men per company. Again, these numbers assume no one from the cavalry at the depots, and so must be considered optimistic.
These averages, while general and somewhat arbitrary, seem to bear out. Company E, 2nd US Cavalry is listed in returns by General McDowell on July 16, 1861 with 4 officers and 56 men present for duty (OR, Ser I, Vol 2, pg 309). Even at the first battle of Bull Run one of the seven companies of Regular cavalry was commanded by a lieutenant. Just before the battle of Wilson’s Creek the four companies of the 1st US Cavalry under Major Sturgis are listed at a combined strength of 250 (OR, Ser I, Vol 3, pg 48).
The true extent of the shortages will be revealed by the muster rolls, but these numbers in the meantime are themselves revealing. And this is before the resignations and battles started.