For year  2022 I have contributed $6000 for  ROTH IRA  and my spouse started working in the middle of 2022, our combined household income for 2022 exceeded Roth contribution income limit and made me ineligible for Roth IRA contribution.  

I realized this in Jan 2024 and asked my brokerage to remove the contribution of $6,000 as it's excess contribution. They removed $6,043 as excess  and generated a form 1099-R for 2024 in Jan 2025 with  Roth IRA distribution of  $6,043 with Code J,. When I called them they said they can only specify Code J as they don't keep track of excess removals requested after 2 yrs and asked me to work with CPA.

Now my CPA, put this excess withdrawal of $6,043 as taxable income in 4b of 1099. I keep asking him to remove it from 4b as it's non taxable income and only $43 gains have to be taxed.

I also CPA to generate form 5329 and show only $43 as taxable from distributions. My CPA is saying Code J is not allowing their system to report $6,043 as non taxable.

Any advice on how I could show only $43 as taxable in 4 b in 1099 and not have entire 6,043 taxable? Even though 1099-R has code J can I use form 5329 and put only $43 as taxable in 4b) of 1099?