1. [of pears] was 2. [above the stage] work 3. [in the bleachers] is yelling 4. [near the shore] were damaged
Prepositional phrases specify a place or a kind of something. A prepositional phrase refers to any set of Preposition + Object or Preposition + Article (the, a, an) + Object that acts like a preposition. When choosing the correct form of the verb, refer back to the Subject of the sentence (in this case, Box, Lights, Fan, Buildings) to determine wether to use a singular or plural verb.
The central theme of Number the Stars is the difficulty of growing up. One could make the case that Lowry uses the context of World War II as a way of making these difficulties stand out clearly.