Rather than guerrilla warfare, you might consider the Reconstruction period one of political terrorism.

Now, /u/Bernardito can come in here and tell me I'm wrong 10 ways from Sunday (and probably be right), but I draw the line between the two in terms of their goals. I see guerrilla warfare as seeking the overthrow of an opposing government or force, whereas terrorism is focused on the subversion of that force from the inside out, exerting pressure through fear rather than direct military action.

Eric Foner is the 800-pound gorilla of Reconstruction study, and if you're interested in this period, I'd encourage you to read his work. Reconstruction is generally defined as the period between 1865 and 1877 when the victorious Union attempted to institute equality under the law in the defeated South. Rather than large-scale battles featuring hundreds of armed men, the fights of the Reconstruction era were in the courtroom and legislatures, and when fighting did break out, it took place in dark alleys and dim fields, with short and bloody clashes between handfuls of men.

The goal of groups like the Red Shirts, the White League, the Knights of the White Camelia and yes, the Klan, was to instill fear and disrupt the government. These groups believed (correctly) that if they deterred black voters from organizing, that if they could disrupt the activities of the Republican Party, the Freedmen's Bureau and other government agencies seeking equality (or something close to it), then they could rally white Southern voters to win at the ballot box what they otherwise could not on the battlefield.

In Foner's classic 1982 paper Reconstruction Revisited (It's free to read on JSTOR, and you should read it if you get the chance), he describes how "traditional" Reconstruction historiography was dominated by an interpretation that portrayed President Johnson as a hero who stood against the nasty Radical Republicans and those evil carpetbaggers. The modern interpretation shows that as absurd and false. The "Radicals" were right in seeking equality between black and white, and when they overrode Johnson's veto of the 1866 Civil Rights Act, it was a triumph, not a defeat.

Nevertheless, you can still see signs of that traditional, racist interpretation on signs across the south. Take the Louisiana historical marker erected in 1950 at the site of the Colfax Massacre and still standing. Foner calls that event the bloodiest single act of violence in Reconstruction. It declares that the event, "at which three white men and 150 negroes were slain ... marked the end of carpetbag misrule in the state."

I'm far from an expert on the subject but I know there were numerous, loosely affiliated white, anti-Republican and white supremacist movements that emerged in the Reconstruction Era. These included groups such as the White League, the Red Shirts and (like you mentioned) the Klu Klux Klan. They were made up of Civil War veterans and primarily targeted Republican officials, African Americans and, in particular, Black Voters. The White League was quite powerful for a time and had membership ranging in the thousands. They operated mainly in Louisiana's Red River Valley and even managed to rout a Union militia at the Battle of Liberty Place in 1874. Like the KKK they participated mainly in massacres of emancipated slaves.

The direct successor of Quantrill's Raiders, the James-Younger gang engaged in acts of banditry throughout Missouri and surrounding states during the late 1860s and early '70s. Though more a gang of outlaws than dedicated Confederate partisans, the James-Younger Gang continued the guerrilla activities of Quantrill's Raiders and largely targeted union authorities, robbing stagecoaches and banks. Jesse and Frank James and the four Younger Brothers were all former Confederate soldiers.

While I don't know of any groups that worked to reestablish the actual Confederacy as a political unit, the years after the civil war saw a very high level of political violence meant to return the South to the previous status quo. This includes militias/armed white groups using violence to overturn elections.

One event that is close to what you're looking for occurred in New Orleans in 1874. The Crescent City White League, led by former Confederate officers, marched thousands of whites to the state house in order to seat their chosen Democrat as governor. There plans were not a secret. On September 13th, 1874, the day before the attack the white conspirators had taken out ads in local newspapers proclaiming the time and place of the coup. The White league then set up barricades around the city and clashed with the Metropolitan Police and the Louisiana State Militia, many of whom were black. The invaders were threatening enough that the governor fled his office and holed up in the local customs house. After they gained control of the streets, they then went through police stations and armories raiding weapons and munition. The governor fled his office and, since the majority of the state's defenders had left there post, no longer existed by the next day.

While this incident was between well-organized forces, much violence was less well planned, but no less political. I think it's important to note that while angry whites may not have formed secessionist militias, much of the organized and unorganized terrorism was to gain political control. For example, historian Douglas Egerton estimates says of all the racial violence that occurred in the tumultuous year of 1873, 1/3 happened during election weeks.

Sometimes the political violence took the form of riots. One of the earliest and worst incidents was on May 1st, 1866 in Memphis. The day previous, federal troops, the only force keeping violence in control, had left the city. According to Egerton:

Furious that wealthy whites preferred to hire black porters and hack drivers, working-class whites and immigrants first assaulted black veterans , and then turned their rage on these institutions those soldiers had protected: schools and churches. Activist William Wells Brown, who was then in the city, witnessed arsonists cheering for “white man’s government.” Determined to restore their lost antebellum world, other whites forced black women to cook meals for them before raping them and burning their homes to the ground. Two days of disorder followed, during which the city government did nothing to quell the violence and assisted in organizing the mobs; one policeman warned blacks that “Your old father, Abe Lincoln, is dead and damned.” By the time rioters finished their work, forty-six blacks had been murdered, another seventy wounded, with four churches, twelve schools, and ninety-one homes destroyed. “Soon we shall have no more black troops among us,” the Memphis Avalanche bragged. “Thank heaven the white race are once more rulers of Memphis.”

And then there is the KKK. Grand Wizard Nathaniel Bedford Forrest, while spreading the Klan's unique form of LARPing, was expressly political. He linked the need for the organization to counter the local government dominated by "Ignorant ex-slaves, organize by city councils and state legislatures, and dominated by carpetbaggers who came from the North to plunder the South".^1 If the Crescent City White League looked to reverse elections, the Klan's violence was often directed at influencing the outcome. This was

David Blight, in Race and Reunion: The Civil War in American Memory, notes that 10% of black members of constitutional conventions in the post-war south were murdered. Other examples from the book are:

in October 1870 in Greene County, Alabama, where four blacks were killed and fifty-four wounded, or another in 1870 in Laurens County, South Carolina, where after Republicans won a local election, some 150 blacks were chased from their homes and thirteen murdered. In South Carolina alone, from the fall elections of 1870 to April 1871, formal testimony recorded some thirty-eight murders and hundreds of whippings. In Meridian, Mississippi, in 1871, local black orators were arrested for delivering “incendiary speeches.” At a court hearing, gunfire erupted, and the white Republican judge and two defendants were killed. In a day-long riot that followed in Meridian, some thirty blacks were slaughtered by mobs.

So while militias groups to reconstitute the confederacy were rare (or non-exsistant), organized political violence to overturn elected governments and institute white rule was not.

Blight, David W. Race and reunion: the Civil War in American memory. Belknap Press, 2001. Egerton, Douglas R. The Wars of Reconstruction: The Brief, Violent History of America's Most Progressive Era. Bloomsbury Publishing USA, 2014. Hurst, Jack. Nathan Bedford Forrest: A Biography. Vintage, 2011. Hogue, James Keith. Uncivil War: Five New Orleans Street Battles and the Rise and Fall of Radical Reconstruction. LSU Press, 2006.

The American civil war.

Be mindful that you're addressing an international audience many of whom would associate the term "The Civil War" with their own country's civil war and not necessarily the American one.