I have already gotton a great start on the Reinforcement script that I will use with each of the Civil War scenarious, updating it through the end of 1863.
It is very easy do do because the forces you need to indentify are mostly already contained in the Order's of Battle from the Wiki. There are other good sources, such as articles on the Army of Northern Virginia, that supply the organizations (and units) of the Army over time.
I am going to be handling all reinforcements with a script as opposed to using Auto Raise, and Auto Up Grades. Therefore, troops may not come into game play at an exact historical date or location by design.
Throughout most of my scripts for other games, I have been using a fixed date for entry into the game but also specifiying several alternate locations for entry, that the game system will choose at random. So, depending on where reinforcements actually arrive, this method best simulates delay.
This modular approach allows many game types to be constructed without having to redo anything. First, a pure battle, of just a few month's duration, without any refinforcements. Or, a Battle Campaign of 18-24 months with a starting OOB of the battle but allowing the next's battle's reinforcements to enter into the game over its duration. (like First and Second Bull Run). Or, a complete 1861-1865 Campaign.
So, the first one was the 1861 Bull Run Campaign, which starts May 1861, just after Fort Sumter and lasts to the end of 1862, and during that time new volunteers flood into both armys. It is a very challenging and fun campaign, with lot's of force crammed into Virginia and Maryland. Supply is more accute for the Confederates, as you might expect, and this fact is well simulated by the game.