[SCDogPapa]

And also, back then, didn't each state put out troops as a unit with a federal commander but remained identified by it's home of origin... (54th Massachussett's, Tennessee Volunteers, etc) Was there not a centralization of military command structure resulting from the civil war... I think each governor still remained in command of his state's militia but the federalizing of troops started during and resulted from this conflict (please confirm)

That's correct.
Below is a link that should answer more of your questions. This is a very large site, with lots of information. The War is really misunderstood by most people. After being fed the winners side throught my school years, I found things to be quite different a couple of years ago. The facts and information are out there, you just have to look for them.

The American Civil War Homepage

[Non-Sequitur]

That's correct.

I don't think that is correct. Washington federalized the Pennsylvania militia to put down the Whiskey Rebellion. Federal militia units were also federalized for the War of 1812 and the Mexican War.