The Anasazi settlements at Chaco Canyon were built on a spectacular scale with more than 75 carefully engineered structures, of up to 600 rooms each, were connected by a complex regional system of roads.
A. with more than 75 carefully engineered structures, of up to 600 rooms each, were - "were" is a verb with no subject.
B. with more than 75 carefully engineered structures, of up to 600 rooms each, - "of up to 600 rooms each" is just modifying the structures so just ignore it. "connected" the ed verbal modifies the noun "75 carefully engineered structures."
C. of more than 75 carefully engineered structures of up to 600 rooms, each that had been - "each" is a subject with no verb. Moreover, it refers to "rooms" which is wrong.
D. of more than 75 carefully engineered structures of up to 600 rooms and with each - this means that the scale is made up of structures rather than using structure as an example. Also it suggests that each room is connected by roads which is wrong.
E. of more than 75 carefully engineered structures of up to 600 rooms each had been - run on, wrong meaning.