If Captain America had fought in the AMERICAN Civil War (emphasis on "American" to distinguish between the Civil War that actually took place and the Marvel event), would he have fought for the North or the South.

I would say the North because I can't picture Cap fighting for slavery.

Union. Steve would never fight for something like slavery.

But what about the time where Cap became Nomad because he thought the federal government was too corrupt? Or when he joined the opposition in the Marvel Civil War because of the Superhuman Registration Act? Do you think that Cap would see the government as forcing the South to give up slavery as the government usurping too much power and would fight for the South since they called for more freedom?

Cap beimg from the north would most likely side with the north against the south.