'Quarried from a site over five miles away' should modify the stone blocks, not the scientists. Therefore, A & C are out.
In B, the present continuous tense is used. That's not correct. Present simple should work.
In E, 'are still a puzzle' doesn't make any sense. Also,
due to is used before a noun. Here it's a phrase.
IMO OA should be D
A.
scientists are still puzzled as to how the prehistoric Britons managed to transport the massive stone blocks of Stonehenge over such a great distance without machinery.
B. the massive stone blocks of Stonehenge
are still puzzling to scientists because of how the ancient Britons managed to transport them over such a great distance without machinery.
C.
scientists are still puzzled by how the prehistoric Britons managed the transportation of the massive stone blocks of Stonehenge without machinery over such a great distance.
D.
the massive stone blocks of Stonehenge still puzzle scientists, who wonder how the prehistoric Britons managed to transport them over such a great distance without machinery.E. the massive stone blocks of Stonehenge
are still a puzzle to scientists due to
being transported over such a great distance without machinery.