Related to the after tax basis, are you saying that the after-tax amount is somehow not properly handled by my method of modifying the 1099R? I did confirm that the after tax amount is indeed NOT reported on form 1040 as taxable income as related to the conversion to a Roth. I'm not aware of the after tax amount being used anywhere else. It doesn't appear that it would be carried forward to future years as it is only relevant to this years taxable income.
