Here are the correct answers for each sentence:

1. The pupils **E) had not written / had cleaned** the sentences yet, the teacher **cleaned** the blackboard.

2. Henry **A) visited / had gone** Puerto Rico before he **went** to St. Thomas.

3. The company **C) ordered / begins** some new equipment before the strike.

(Note: "equipment" is an uncountable noun, so "equipments" should be corrected to "equipment.")