1. It is best to make the payment at the IRS website for the 2024 amendment.
2. The earnings are allowed to stay in the Roth IRA since it is after the due date and your are paying the 6% penalty. You do not need pay taxes on the earnings.
3. Yes, in your case it will be just code J (assuming you are under 59 1/2) since this is a regular distribution. You removed the excess after the due date, therefore it is a regular distribution with code J. Code P and J are only used if you request the withdrawal of the excess plus earnings by the due date.
You will remove the excess amount of $3,500 as regular distribution (ignoring any gains or losses) and they will distribute exactly $3,500.
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