Thank you @klawaz-gmail-com.
As you had the excess contribution returned to you in June 2023 (no gains) this is before the extended deadline of your original return, so no penalty should be incurred.
Yes you need to file a 1040-X amended return including the Form 8086 to show a $0 contribution and corrected IRA basis.
You will need to print and mail your form 1040-X and hand write on the top "Filed pursuant to section 301.9100-2."
After reviewing Instructions for Form 5329 it does not appear you will need to include this form in the amended return.
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