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Final solution at one place:

Important: The purpose of this post (and all the other posts by me) is to give a complete solution to all GMAT-Prep Verbal questions at one place. Sometimes students have to wade through dozens of posts to get to the final answer. My posts will give one complete and crisp solution required to arrive at the correct answer by eliminating the wrong ones. Some of the content in these posts may have been taken from various other sources (discussion forums).

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
(B) with more than 75 carefully engineered structures, of up to 600 rooms each,
(C) of more than 75 carefully engineered structures of up to 600 rooms, each that had been
(D) of more than 75 carefully engineered structures of up to 600 rooms and with each
(E) of more than 75 carefully engineered structures of up to 600 rooms, each had been

In this construction, 'scale of' is the wrong idiom. 'Scale of' is correctly used in constructions such as: 'on a scale of 0-10'. This eliminates C, D, and E.

In A, if we remove the nonessential part between the commas, we are left with:

The Anasazi settlements at Chaco Canyon were built on a spectacular scale with more than 75 carefully engineered structures were connected by a complex regional system of roads.

In A, we can't use 'were' ... 'were' without a connecting word (such as 'and / or / but / that etc. depending upon the meaning'). In this sentence, the 'structures' were 'connected', so we surely need some connector (preferably 'that') between 'structures' and 'were'. Or else, A becomes a run-on sentence. It tries to have two main verbs without using any sort of subordinating element. If you take out modifiers, adjectives, etc., you're left with the following: the settlements were built with structures were connected. UGH!

Similarly, E is a run-on sentence.

In B, if we remove the nonessential part between the commas, we are left with:

The Anasazi settlements at Chaco Canyon were built on a spectacular scale with more than 75 carefully engineered structures, connected by a complex regional system of roads.

In the sentence above, the last part is a non-essential modifier. Perfect.

In C, D, and E, 'scale of' is the wrong idiom.
Also, in C, we can't use the past perfect ('had been') as the events don't have a time lag.