"that' not 'it"! If it's the first time you are asking someone to repeat something, use "again". If they've already repeated it, it would be ok to use "one more time". I'm sorry, could you please repeat that? (the first time) I'm sorry, I still didn't understand. Could you please say that one more time? (if the second or later)

They are both okay. However, it would be more natural to say "I'm sorry can you repeat that again?" I recommend using "please" in both as well.

Yes

Thank you!

Either is fine. “I’m sorry, could you repeat that again please?” or even “I’m sorry, could you say that one more time please?” Are probably more common.