If something is unclear,than it is not a hard fact.So,it would be easier to just post hard facts,that we know of as today:
FACT - Patsy Ramsey called 911 on the morning of Dec.26,1996,claiming she discovered her daughter gone,and there is a ransom note.
FACT - Boulder police arrived,and after a cursory search outside the house,found no force entry,or footprints in the snow.
FACT - Patsy,John and Burke were in the house from 10:00 pm until the following morning,when police were called.
FACT - Two couples who were close friends were called by the Ramseys'to come to the house the morning of the 911 call.Rol Hoverstock(pastor),and Dr. Beuf (JonBenets' pediatrician),was also there.
FACT - The call from the kidnappers never came.
FACT - Burke Ramsey was taken from his bedroom,and taken to a neighbors house.
FACT - John,after being asked by a detective to search the house,found the body of JonBenet in the basement,which he carried upstairs,and put her on the floor,just outside the basement door.
FACT - John Ramsey was heard by one of the authorities,making a call for arrangements to leave Boulder Colorado,to go to Atlanta,Georgia.
FACT - A few hours later,the Ramsey's were asked by the LE to leave the house.They stayed with various friends for a few days,until they ended up staying with the Stine family for several months,before leaving for Atlanta.
FACT - The autopsy confirmed that JonBenet was choked and her hands were bound by the same cord,the cord also had a broken paintbrush attached to it. The autopsy also confirms that JB was bashed in the head.Abrasions were found in three separate areas on JB's body,which later Dr.Meyer said could be consistent with the marks of a stungun. Markings were on the palm of JB's hand,which Dr. Meyers' believes is a drawing of a heart done with a red pen.
FACT - DNA found in JB's panties were tested to confirm it is not the DNA of a Ramsey male.
There may be more,but that's all I can think of at this moment of HARD evidence,anything else is either inconclusive or disputed.