"2022 Contribution
I withdrew the 2022 amount and paid penalties for both the year by filing 5329 for 2022 and 2023 in 2024. IRS the assessed additional penalty for early withdrawal which I paid as well. However, I didn't include the 2022 contribution as basis in the 2023 8606 form."
Something is wrong here. There is no early distribution penalty involved in this. It's impossible for the IRS to have assessed an early-distribution penalty on a distribution made in 2024 since your 2024 tax return is not yet due. Perhaps what you were charged was interest on the late payment of the excess-contribution penalties.
1 and 2. Roth contributions are not reported on Form 8606. Nothing that you have mentioned is reportable on a 2022 Form 8606.
3. The taxable amount of the code-2 Form 1099-R that reports the Roth conversion is determined on Parts I and II of your 2024 Form 8606. All of the calculates are done on that form. You do not do any separate calculations outside of that form.
4. As long as you file the 2023 Form 8606 showing the correct addition to your basis in nondeductible traditional IRA contributions, you can ignore the code-R 2024 Form 1099-R.
