OK, the you did get two Forms 1099-R (even though they might be on the same sheet), one with code J and the Other with codes P and J. That makes sense now.
Your 2016 tax return needs to be amended to report the 2016 excess contribution adding 2016 Form 5329 calculating the 6% penalty. Your 2017 tax return return needs to be amended to add the code PJ 2018 Form 1099-R to include the box 2a amount in income and to include 2017 Form 5329 to again report the 6% excess-contribution penalty on the excess still in there from 2016 and to calculate the 10% penalty on the box 2a amount.
You'll also need to enter the code PJ 2018 Form 1099-R on your 2018 tax return to get credit for the tax withholding on box 4. The code J 2018 Form 1099-R must also be reported on your 2018 tax return with the zero taxable amount calculated on Form 8606 Part III and to reduce the excess contribution on Form 5329 carried in from 2017 to zero.
