The correct option is A Had gone over
The given sentence expresses a situation which would have happened (he would have passed the exam with flying colours) if a certain action had happened in the past (If he had gone over his lessons). This type of sentence is called type 3 conditional sentence. It refers to a condition that was likely but did not actually happen in the past. In such conditional clauses ('starting with 'If'), the verb is used in past perfect tense ('had'+past participle). The past participle form of 'go over' is 'had gone over'. Hence, option A is correct.
Option B: The phrase, 'would have gone over' is not used along with the conditional 'If' clause. Hence, option B is incorrect.
Option C: The phrasal verb, 'went over' is in simple past tense. It is not in past perfect tense and cannot be used in a conditional clause starting with 'If'. Hence, option C is incorrect.
Option D is incorrect as option A is the correct answer.