@AMS2022 IMO, Box 1 of the 1099-R for the excess deferral should be $2,900.98 with a distribution code "P" and there should be a second 1099-R for the $50.19 earnings. The reason for two 1099-R's is that the excess deferral is taxed in the year of contribution while the earnings are taxed in the year of distribution.
I reread your OP. There are a couple of problems in your situation.
First, the 2022 excess deferral was not distributed by April 15, 2023. Secondly, the excess plus earnings came out of your wife's rollover IRA, the IRA trustee may not know or care whether the excess was an "excess deferral" or an "excess contribution". As a result, the IRA trustee may treat that as an "excess contribution". If so, they may simply lump everything together and issue just one 1099-R for $2,951.17 with a distribution code 8 in Box 7. So it's imperative that you talk with IRA trustee on how they will issue the 1099-R before you do anything.
Finally, I want to point out there is a difference between "Excess Deferral" and "Excess Contribution". I believe you're situation qualifies as an "Excess Deferral". I'm assuming your wife put in no more than the 401(k) limit of $20,500 (or $27,000 if she's age 50 or older), was an executive at the company where she worked and her 401(k) contribution was subject to some sort of "top heavy" rules.
If the $2,900.98 were an "excess contribution", then that would be taxed in the year of distribution, in other words, it would be taxed in 2023 and no 2022 amended tax return would be required.
If your main purpose is to limit penalties and interests, you can always pre-pay an estimated amount equal to $2900.98 multiplied by your tax bracket at www.irs.gov. But that's probably not worth the potential hassles.
Here another link for your reading:
https://www.mysolo401k.net/removing-excess-deferrals-when-contributing-to-multiple-retirement-plans/
