It seems that you should be filing Form 990-T on behalf of your IRA to claim a refund paid to the IRA of the backup withholding.
See the instructions for Form 990-T with regard to the special instructions for a claim of refund of backup withholding: https://www.irs.gov/pub/irs-pdf/i990t.pdf
There is no Form 1099-R involved in this because this tax withholding was not a distribution from the IRA. The tax withholding was made on behalf of the IRA, not on your behalf. (IRAs can incur a tax liability if they incur Unrelated Business Taxable income, but that doesn't seem to be the case here.) This has nothing to do with your individual tax return.
