You are correct to be concerned since any pre-tax premiums are indeed not allowed for the HTCT.
"the part I'm not sure about is the premiums are paid pre-tax from her pension payments."
The problem is that we in the Community have no way to know if the premiums paid for your health insurance are pre-tax or not. Does your wife's pension cover her health insurance premiums? If they are listed in box 5, then they are tax-free.
However, are your premiums also listed as part of box 5? I could well imagine that there is a separate worksheet that comes with the 1099-R that shows your premiums coming out of the distribution in box 1 and is included in box 2a as taxable.
But we have no way of knowing. Please call her pension administrator and ask if your payment is pre-tax or not.
Sorry not to have a more concrete answer.
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