Yes, you are too late. You're penalized if you make withdrawals before 59 1/2 under most circumstances. You'll owe a 10% penalty on the taxable portion of the distribution. It's not a matter of just removing the nontaxable amount at this point. If you had taken it out before April 15, 2022 there would have been no penalty.
IMPORTANT: You must track this nondeducitble contribution until you retire. If you did not file Form 8606, you need to file it now and it can be filed alone because it is a signature document. Since you did not request the return of contribution by the due date of your return then you will have to file Form 8606 to report this nondeductible contribution (basis). When you later take distributions/convert funds to Roth, you will need the basis information from line 14 of Form 8606
How are non-deductible contributions taxed?
If you made non-deductible contributions, then any distribution contains both a taxable and a nontaxable portion. The nontaxable portion is based on your cumulative after-tax contributions, and the taxable portion is based on the money those contributions earned over time.
For more information about your nondeductible contribution to your IRA click this link: What is Form 8606?
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