No need to amend your returns. You can file form 8606 by itself, without the 1040X.
File a separate 8606 for each year that you made a non deductible contribution. The IRS can charge a $50 penalty for filing it late. Include a cover letter with your 8606s explaining why you are filing late and asking for a waiver of the penalty.
You can find prior year form 8606s here:
https://www.1040.com/tax-tools/forms-publications/
