The sentences that use a comma in a way that could be considered contested usage are:
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Stephen did not understand the question, and so Gina tried to explain it to him more clearly. (The use of "and so" can be debated; some writers prefer to avoid a comma before "so" when it connects two independent clauses.)
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We are passing through New Orleans, Louisiana right before we stop in Houston, Texas. (The commas between the city and state can be contentious since some style guides advocate for including a comma before "right," while others do not.)
The other sentences reflect standard, generally accepted uses of commas.