Let's try to get the meaning of the original sentence.
In the cross section of the molar,
the widening of the periodontal ligament and
adjacent bone loss was shown.
What's shown?
the widening of the periodontal ligament + adjacent bone loss
These are two different things.
The widening of adjacent bone loss is nonsensical.
Thus, we need 'were' (and not 'was') to correctify the original sentence.
(A) In the cross-section of the molar, the widening of the periodontal ligament and adjacent bone loss was shown.
Incorrect for "was"
(B) The cross-section of the molar showed widening of the periodontal ligament and adjacent bone loss.
Writing in passive :
Widening of the periodontal ligament and adjacent bone loss were shown by the cross-section of the molar.
Looks correct. (C) In the cross-section of the molar, the widening of the periodontal ligament and adjacent bone loss were shown.
The widening of X and Y - implies the widening both X(the periodontal ligament) and Y(adjacent bone loss).
The widening of adjacent bone loss - is nonsensical.
(D) Both the widening of the periodontal ligament and adjacent bone loss was shown in the cross-section of the molar.
Incorrect for "was".
(E) The cross section of the molar having shown widening of the periodontal ligament and adjacent bone loss.
"having...." just modifies cross section of the molar. It's a sentence fragment and not a complete sentence.
IMO
B