Take another look at the sentence:
Poking his head through the unzipped top, store after store was visited by Freddy the Chihuahua as he rode in Jodi’s book bag.
Poking his head through the unzipped top, a participle phrase, comes right before store, an illogical target. The dog, not the store, has a head!
Before you continue, review the rules for misplaced and dangling modifiers.