Let's remember that a 1099-R is for money Out. Not for what is or isn't basis, is or isn't taxable, was or wasn't kept, rolled, converted.

"- 1 for the 2023 Gross Distribution $7487 coded N with no amount in Box 2a"

This would be for the 2023 tax year contribution + net income allocated to that excess contribution. Since that was removed before the tax year filing due date, the contribution error is moot. You only deal with the earnings.

"- 1 for the 2024 Gross Distribution $8498 coded R with no amount in Box 2a"

Same as above, for tax year 2024 contribution.

"- 1 for $16486 with the same amount in Box 2a"

Did your taxpayer then make a Backdoor conversion for all of this? That would be why there are three 1099-R.

"has no other Traditional IRA accounts"

Trad IRA, SEP IRA and SIMPLE IRA accounts are all aggregated for purposes of conversion.

"Is the $16486 fully taxable or only the earnings?"

As long as the original contribution was never deducted, contribution is Basis. The earnings are not, they were never taxed.

"These contributions were funded out of non-qualified funds/post tax money"

The source of the funds doesn't matter. There are no non-qualified funds; you could sell drugs or mow lawns, but as long as you are eligible to contribute, you can use the money for a contribution. About the only "nonqualified" funds I can think of is if they tried to Rollover an RMD. An RMD can fund your contribution, because once it's taken as an RMD, it's just your money. You can't call it a Rollover, though.

"and the full amount is showing as taxable."

The initial contribution to the Roth is moot (recharactized in time), and becomes basis. So, remember: there is no contribution to Roth. There is only contribution to Trad IRA, and it is Basis, and for the conversion, you need to enter Basis, so that it is the nontaxable portion. Did you mark Conversion and enter Basis?