It's quite possible that will get no acknowledgement from the IRS for the late Forms 8606 that you filed.

Prepare your 2016 tax return based on the assumption that the IRS has received and processed your late forms.  Your 2016 tax return is required to include Form 8606 to calculate the taxable portion of your distribution.  For the amount of your nondeductible contributions carried into 2016 from years prior to 2016, enter the total nondeductible contributions shown on the most recent year's From 8606 that you filed in January (usually line 14 of that form).