It is very likely that the missing 1099-MISC is the reason or part of the reason for the IRS delay in processing your return. You need to wait for the IRS to either process your return or send you a notice advising you of any discrepancies they found on the return or requesting additional information.
If the IRS processes your return, once it has been processed, you will need to file an amended return to include the 1099-MISC.
If the IRS sends a notice requesting additional information and the situation is resolved in that manner, you would not need to amend your return.
If you did not file a NY return with your original federal/state returns, you may need to file a NY return once the IRS processes your return.
The $589 penalty was likely triggered because the tax software, by default, assumes your income—and therefore your tax liability—is spread evenly across all four quarters. A large conversion in the last week of December would create a significant tax liability for the fourth quarter. If your estimated tax payment for that quarter, paid in January 2025, covered this liability, you should not be penalized. You would need to amend your return to use Form 2210, "Underpayment of Estimated Tax by Individuals, Estates, and Trusts." On Form 2210 you would select the annualized income installment method which allows you to calculate your required estimated tax payments based on when you actually earned the income. This will show a much lower income for the first three quarters of 2024 and a significant increase in the fourth quarter due to the Roth conversion.
Regarding the Roth conversion, I would wait until the original return is processed or resolved by the IRS before making any changes.
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