Q1. Yes, 2017 was the beginning of calculations.
Q2. Any forms submitted without the correct basis should be corrected. Since you forgot the IRA existed, I don't know that you can go back and correct forms without the account information.
Q3. You are very impressive to be filing this each year on your own. Great job doing the right thing!
That is odd for the IRS to return the 8606. At the end of the day, all you can do is your best and keep records to help explain any discrepancies.
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