1. If your employer reported the $1000 contributions on your W-2, then you would not enter the amount anywhere else. This would be reported in Box 12 with a code W. If this was not your case, then comment here so I can direct you to the appropriate section.
2. Yes, do enter your after-tax medical expenses in the medical section on schedule A. The total medical expenses will need to exceed 10% (7.5% for those born
before 1/2/52) of your AGI to receive a benefit. This is not double-dipping at all, because you took no distributions from your HSA. It is a smart retirement strategy to maximize the tax benefits of an HSA.
3. You have a choice to make. If you do reimburse yourself for 2016 expenses from the HSA fund, then you will only be able to deduct the portion of medical expenses that exceed your HSA disbursements on the schedule A. If the $1000 difference doesn't meet the 10% AGI threshold, then no deduction on schedule A. If you decide to go this route, then make the choice by the due date of the return 4/18/17.
If you wait until the surgery date and pay for the surgery with your HSA fund, then you will empty the fund balance for qualified medical expense and have no fees to pay May 1st. Next year, you will receive the 1099-SA for the disbursement.
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