Looks like we have a veritable Civil War mystery, eh Josh? How did Companies acquire their lettering? I guess there are deeper and more meaningful mysteries to be solved, but I can't help but wonder about little rules minutiae like this! :-)
I guess how the Company lettering occurred isn't terribly important as it was probably somewhat random, maybe based on the order by which the Companies came to camp when the Battalion was first being formed. As for the 3rd senior captain being the commander of the Color Company (irregardless of the designated letter of the Company), that makes sense too - the first two senior Company commanders would be of much greater use handling the Flank Companies as these were the Skirmish Companies of the Battalion, a rather critical component of Battalion combat. Were I a Battalion Commander, I'd want my two most experienced (in theory) commanders handling the complex affairs of the skirmish line. Protecting the colors was truly important too, from a morale standpoint, but one that the next most experienced/senior commander could handle without undue trauma.
As for the Battalion's Companies coming onto line, I think you solved a minor mystery for me. I always wondered why a Battalion would post Companies on the Flanks first, then fill in the Center with the remaining Companies. To me, that always seemed to be a disaster in the making. What if the spacing between the Flank Companies wasn't adequate for the remaining 8 Companies, or too wide? Why not form the Battalion from flank to flank so as to preserve the order and not complicate things anymore than combat would? Your opinion (which is probably fact) that Hardee's/Casey's manuals were pointing out how the Battalion would be formed on PARADE, via Companies approaching the parade ground in order of the seniority of the Company commanders, as opposed to how it would be formed on the field of combat, truly makes a lot of sense. Thanks for that insight, one with which I wholeheartedly agree. Once the Battalion had been formed on the parade ground, it was to keep that order of its Companies and maneuver and fight accordingly.
10th Co------9th Co----------8th Co-----------7th Co----------6th Co---------ClrGrd5th Co---4th Co--------3rd Co-------2nd Co-------1st Co
2nd Capt-----7th Capt--------10th Capt--------5th Capt--------8th Capt-------3rd Capt-------9th Capt------4th Capt-----6th Capt-----1st Capt

By any chance, do you have any insight into the other questions I had asked, such as: are those selected for the Color Guard replaced in the Companies from which the Guard was formed (thus keeping these Companies up to strength), or were the affected Companies forced to deal with the diminished manpower, however small the decrease might have been?
I'm enjoying this thread immensely, and I'm learning a little bit more each and every time.