It is interesting to note that the South possessed a majority of the major ports in the United States which brought in 75% of the tariff revenue that the U.S. government collected [a big reason for not allowing secession because tariffs were the largest source of federal revenue as there was no federal tax at that time]. So, "reintegrating" the South was no small problem as it had been extremely prosperous in its importing and exporting, and now entire plantations were destroyed and burned. Added to this, Atlanta had been burned to the ground by a vindictive and sadistic General Sherman; every single family in the South had suffered at least the loss of one male family member, plantation owners were bankrupt as confederate money was worthless and their places sold for the taxes, soldiers returned home starving and diseased, and freed slaves were homeless and also starving, as well.
After the Civil War, the nation was still greatly divided because the South had been devastated physically and spiritually. Besides the destruction of the land, homes, and cities, no confederate soldiers were allowed burial in Arlington Cemetery, and many of their bodies were lost to their families. Carpetbaggers, opportunists from the north, and scalawags swindled people out of their property, exploited the poor, illiterate, and naive former slaves, giving them false promises of "forty acres and a mule" and manipulating them for their own political purposes.
It is only in the twentieth century that the South has again become an economic force. Still, many Southern states are among the poorest states in the nation. The President responsible for more deaths of American soldiers than any president in U.S. history [approximately 650,000] was killed before he could rectify in any real way other than emancipation the harm done to America.
For the nation as a whole, the only real problem (that was connected to the Civil War, at least) was how to get the South reintegrated into the country. The country had to decide what conditions to impose on the South before it would be allowed back in. It had to decide, in that context, what to do with the freed slaves. What rights should they have? How much, if at all, should the government help them?
Though this did not affect the whole nation, the South also had to figure out how to reorganize its economy. There was no more slavery now. So what would the South base its economy on and how would it find laborers?