After you file

"they took out too much"

 

You need to wait for the actual 1099-R(s) that you will get for you and your spouse.

 

The simplest solution is to amend 2023 next year. with the forms they send you.

The code(s) may not be what you expect.

If the codes cause further problems you would have to direct TurboTax using the corrct codes and explain to the IRS why you are filing this way.
OR, there may be no problems or problems small enough not to worry about.

As I stated several times,

"earnings don't go on Schedule D; that [sic] are added into 1040 Line 4b."

Allocable earnings go  on Form 1040 Line 4b, that increases your AGI, 1040-X Line 1.

Your AGI cannot go down, because negative earnings are ignored.

As I stated several times, 

"the 6% applies to the second case, case 2, only. See Form 5329."

Now that you confirm that earnings were removed, on time, you will be amending under case 1.

You know exactly what the custodian earnings calculation was by subtracting your excess contribution from your actual distribution.

You have to do this for each spouse's IRA since you both had excess.

 

When amending and paper-filing,

do not include your old 1040 nor your revised 1040 because the Form 1040-X reflects any changes there and becomes your new tax return.

 

@msv1