1. The tax on the conversion is in your tax liability as the income from the conversion is on your tax return. The penalty is based on the total income vs tax paid during the year. So, yes, the conversion income is part of the penalty computation. If you did the conversion later in the year, annualizing your income may help lower the penalty.
2. To see your forms:
The IRS expects to be paid when you are -so an estimated payment to the IRS would have been a good move.
See Information on Penalties
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