1. Yes, if the custodian refuses to correct the Form 1099-R then you can submit a substitute Form 1099-R with the earnings in box 2a.
2. Removing $29 is fine. Remove it as a regular distribution since it is after the 2023 due date.
3. You will also have to pay the 6% penalty on your 2024 return since the 2023 excess wasn't removed by December 31, 2024. Since you remove the 2023 excess in 2025 as a regular distribution you will get a 2025 Form 1099-R with code J (if you are under 59 1/2) or T or Q (if you are over 59 1/2). When you enter this Form 1099-R next year on your 2025 return you will resolve the excess contribution.
4. No, you should not owe a 10% early withdrawal penalty since you are removing your contributions.
5. This is correct.
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