(A) contains a misplaced modifier:‘Including not only the City of San Francisco and Marin County.’ This modifier should be immediately following by that which it modifies: ‘the Golden Gate Bridge and Highway District.’ It also contains the phrase ‘where within their boundaries the bridge exists,’ which is very vague. And, it contains improper parallelism. The construction ‘not only’ always precedes ‘but also.’ In this case, we have only ‘but.’
(B) corrects the issue of misplaces modifier, uses correct idiom, and maintains the intended meaning
(C) corrects the modifier but is also worded in a confusing manner, and uses the awkward and redundant phrase ‘whose…of which.’
(D) has no grammar errors but changes the meaning of the sentence to indicate that the bridge is included within the ‘Napa, Mendocino, and Del Norte counties, when it is only within the boundaries of San Francisco and Marin county.
(E) begins the same way, but corrects the modifier problem, but keeps the vague language, adds redundancy: ‘but also… as well’ and is a fragment.