Retirement tax questions

Thank you. This is very helpful. Just to make sure I'm understanding correctly:

For years 2021-2024, is the 6% penalty imposed just on the excess contribution amount ($6000) and not the earnings?

For 2025, could you please clarify what you mean by "regular withdrawal of whatever dollar amount"? Do you mean the $6000 plus the earnings? I'm assuming my financial institution can provide me with the exact number. Should I report it now or wait until I file my 2025 tax returns in early 2026? I'm guessing the withdrawal needs to be shown on the 2025 form 5329. 

I'm also reading posts mentioning form 1099-R. Could you please provide some insights on that as well.

@Opus 17