How many people have been killed by the kkk?

We will never know.

Unlike the new terrorist groups out today, the KKK hid behind bed sheets for fear of discovery. They didn't always take credit for their murders. Also consider that they didn't have sophisticated ways to publicize the terroristic acts like we do now. Even if they did, it would be a stretch to assume they'd be smart enough to know how to use them.
Plus, the era they were in full power was also during a time when the government didn't care about black lives (even worse than today, if you can imagine that). So they made little effort to track these things.
And you certainly couldn't expect the KKK to keep an accurate count once the number got past 10. According to the Huffington Post, a recent study puts the number at 3960. That's just for Blacks. Keep in mind that they also hated Jews, Catholics, Republicans (before the switch) and anything intelligent. So I expect the number to be at least 20% higher with everyone included. But this number still doesn't include the killings that we can't prove were done by the kkk. The cop murders where the cop was a secret kkk member
The FBI murders that never made sense
The random poisoning here and there
The dead Black body that was found on the road occasionally in the late 1800s
The strange fruit left to hang from trees in the late 1800s till the mid 1900s.
The many black Church bombings that no one claimed and the cops barely investigated in the early 1900s. So yes it's kinda impossible to know exactly how many.

Slower