# take ... and stone

These commands are addressed to Israel as a group and so are plural. 

# take both of them

"then you must bring both the girl and the man who slept with her"

# because she did not cry out

"because she did not call for help"

# because he violated his neighbor's wife

"because he slept with a girl who belongs to a fellow Israelite" 

# you will remove the evil from among you

"you must remove from among the Israelites the person who does this evil thing" or "you must execute this evil person"