Your statement is very correct that, "Often you could have different companies within the same regiment uniformed differently."

At least early in the war, each company was unformed as soon as possible...usually before being assigned to a regiment. An example related to Shiloh is Company G "Tuskaloosa Plowboys" of the 38th Tenn. Infantry Regt. This company was formed in West Alabama (men from Pickens and Tuscaloosa Counties).

The company was organized at Big Creek Church, in Coker, Tuscaloosa County on the Columbus Road (now U.S. Hwy 82). The men received their uniforms there at the church, when they entered service. The company travelled to Abbington Camp of Instruction, located in Fayette County, Tennessee. There, along with two other Alabama companies, the Tuskaloosa Plowboys were assigned to the 38th Tenn. Having already been uniformed when the company formed, and it being unlikely that they were reuniformed at this point, naturally their uniforms were different than other companies in the regiment.

As to the 38th Tenn. at Shiloh, it has been said that the 38th Tenn. “won more laurels” at the Battle of Shiloh than any other Confederate regiment that fought there. The 38th took at least one thousand Union prisoners near Owl Creek during the battle. One account says that the 38th took as many as five thousand prisoners at Shiloh. The 38th had seven killed, four mortally wounded, forty other wounded, and twenty seven missing during the fighting at Shiloh.