Butler County Prosecuting Attorney Kevin Barbour filed a second amended complaint Friday, adding two counts of forcible sodomy and one count of sexual exploitation of a minor to the case against Shelton, who is being held without bond.
The 45-year-old already was facing two counts of child kidnapping, a count of first-degree burglary, a count of first-degree assault, a count of felonious restraint and one count of armed criminal action in Butler County.
Shelton is accused of kidnapping a 5-year-old girl from her Poplar Bluff home during the early morning hours of Oct. 24. He also is accused of assaulting and restraining his girlfriend when she allegedly found the girl in Shelton's home, where he allegedly molested the girl.
The investigation into the girl's case led authorities to Ripley County, where Shelton is accused of assaulting his girlfriend's father, Curtis Whitlock, after he allegedly found Shelton with the girl in Whitlock's trailer.
Four days before Shelton allegedly kidnapped the 5-year-old, authorities say he kidnapped a 10-year-old Qulin, Mo., girl at knife point and took her to Ripley County, where he has been charged with molesting her.
The Qulin girl's abduction was reported to the Butler County Sheriff's Department the same day, but authorities had no suspects until the girl identified Shelton as her abductor from news photographs of him at the time of the Poplar Bluff girl's abduction.
Shelton is to appear at 1 p.m. Thursday before Associate Circuit Judge John Bloodworth for a preliminary hearing on the Butler County charges.
Shelton was charged with first-degree burglary and second-degree robbery in Ripley County for his alleged actions involving taking the 5-year-old to the Whitlock property. He is accused of entering the Fairdealing, Mo., home, as well as forcibly stealing car keys and a cellphone from Whitlock.
After Ripley County Prosecuting Attorney Christopher Miller filed the charges against Shelton in November, he filed a motion with the court for Barbour to be appointed special prosecutor on the cases.
In addition to the state charges, a federal grand jury handed down a three-count indictment against Shelton in November on two counts of production of child pornography and one of possession of child pornography. He is accused of using a cellphone to produce child pornography of the two Butler County girls he allegedly kidnapped.
No date has been set for Shelton to appear before a U.S. magistrate judge on the federal charges.