"If I look back at my 2023 return, I see $6,500 in the excess contribution section and $390 (6%) as "additional tax"."
You must amend your 2023 to remove that penalty and enter the code JP 2024 Form 1099-R because the amount in box 2a of that form is taxable on your 2023 tax return, not on your 2024 tax return. When going back through the Roth IRA contribution, when TurboTax asks if you had the excess contribution returned before the due date of your 2023 tax return, answer that you had $6,500 of contribution returned.
