First, there is no limit on the amount one is eligible to convert to Roth. A Roth conversion is not a regular Roth IRA contribution.
I'll assume that your wife has no other traditional IRAs.
Because the balance in your wife's traditional IRA on '12/31/2022 was $9, the nontaxable amount of the Roth conversion is calculated as 6,000 * 6,000 / (6,000 + 9) = $5,991, resulting in $9 of the conversion being taxable and $9 of basis in nondeductible traditional IRA contributions remaining in her traditional IRA. Yes, it would have made sense to convert the entire $6,008, leaving $0 in the traditional IRA on 12/31/2022. That should have been on your wife's 2022 From 8606.
For this purpose, all of your wife's traditional IRAs are treated as a single traditional IRA, so there was really no point to opening Traditional IRA (B) for your wife when the $6,500 contribution for 2023 could have just been made to your wife's Traditional IRA (A). Simply convert all of your wife's traditional IRA balances to Roth and if the total amount converted is more than $6,509, the amount in excess of $6,509 will be taxable. The contribution and conversion will be reported on your wife's 2023 Form 8606 with $9 on line 2 carried over from line 14 of your wife's 2022 From 8606.
[Posted before I noticed that Hal_Al already said the same thing.]
This answer has been verified for accuracy by an Intuit expert employee
