To answer the "punctuation inside or outside quotes?" question, ask yourself if the punctuation belongs to the quote or the sentence that contains the quote.
Keep punctuation inside when it's part of the quoted sentence.
If the quoted sentence ends but the unquoted sentence continues, periods become commas.
"How are you doing today?" he asked.
"Check out my quotes," Rob said. "This punctuation seems pretty natural."
If you do it the other way, it's all kinds of wrong.