choice a is a run-on - 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. that's bad.

choice b is correct: it uses a nonessential modifier set off by commas ('of up to 600 rooms each'), which, if eliminated, yields the intact and legitimate sentence ...carefully engineered structures, connected by... (with another nonessential modifier).

choice c:
- 'scale of' doesn't make sense
- you can't say 'each that had...' (can't follow 'each' with a relative pronoun - if you're going to use a relative pronoun, it has to come directly after the thing it's trying to modify)
- no justification for using the past perfect ('had been') - that verb, if there's a verb there at all, should be in the simple past (the same tense as everything else in the sentence, because everything described in the sentence is contemporaneous)
- it doesn't make sense to use 'each' AFTER the comma, because it's not true that each structure was connected with a road system. instead, the road system connected all of the structures with each other, which is nowhere close to the same thing. (having 'each' BEFORE the comma makes sense, because it's actually true that each of the structures comprised up to 600 rooms.)
analogy:
the USA comprises 50 states, each of which is united by a federal government --> wrong (the implication is that each state has its own federal government)
the USA comprises 50 states, all of which are united by a federal government --> correct
the USA comprises 50 states, (all) united by a federal government --> correct, whether you have 'all' or not

choice d:
- 'scale of' doesn't make sense
- the use of AND sets up ostensible parallelism, but the two structures given aren't parallel (one starts with of and the other with with)

choice e is also a run-on sentence (you'll see this if you reduce it to its 'skeleton', a la choice a)