Q1. Yes, you enter $6210 as withdrawn by the due date. You withdrew the 2023 excess contribution after 2024 therefore you still need to pay the 6% penalty on this excess contribution. Yes, the special treatment only applies if you withdrawn the excess plus earnings before the due date. The due date of the 2023 return has passed therefore you will have to pay 6% penalty since the excess wasn't removed by December 31, 2024.
Q2. If this was a contribution made in 2024 withdrawn in 2025 then this will have to be entered on your 2024 return.
Q3 Yes, this is correct.
Q4 Yes. this is correct.
Q5. You do not add a Form 1099-R in your 2023 amended return. The 2025 Form 1099-R with code J will be reported on your 2025 return.
Q6. No, you will enter the 2025 Form 1009-R with code J on your 2025 return. But you can ignore 2025 Form 1099-r with codes PJ assuming it had no taxes withheld.
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