The Krana is controlled by the Bahrag, and the Krana are the brains of the Bohrok. The Bahrag control the Krana, which controls the Bohrok, and Bohrok Va. But, the Krana-Kal is a different story. The Krana Kal can do
anything they want, even disobay the Bahrag. But, the Krana-Kal(which control the Kal) know if they release the Bahrag once they fall, they'll get something in return...
Thats my Krana theory, now onto the Bohrok bodies themselves...
I think that the Bohrok and Bohrok Va were once free creatures, doing anything they please. But, when the Bahrag came into exsitance, they placed special "brain" type of things into the Bohrok and Bohrok Va. Now the Bohrok and Bohrok Va work for the Bahrag. The Bohrok Kal were created in case the Bahrag were brought down by a physical or natural force, and the Bohrok Kal would find out what happened and try to release the Bahrag. But I must note something, the Bohrok Kal were'nt imprisoned, they were destroyed.