CPAs are often not well versed in the parts of the tax code involving less common retirement-account situations.
Assuming that it doesn't affect any other part of your 2016 and 2017 tax returns, such as a mistakenly haven taken Retirement Savings Contributions Credit based on these contributions (it appears that you did not), you might be able to file the 2016 and 2017 Forms 5329 stand-alone, but the IRS sometimes asks that you include Form 1040X and Schedule 4 to show this change to Other taxes and to provide explanation. Either way you'll need to pay the penalty calculated on each of these Forms 5329.
You'll file your 2018 Form 5329 with your 2018 tax return and the penalty on that form will be included in determining your refund or balance due.
With your 2019 tax return you have 2019 Form 8606 Part III reporting the regular distribution and applying your Roth IRA contribution and possibly Roth conversion basis to determine the taxable amount, if any. You'll also have a 2019 Form 5329 reporting this distribution as correcting the excess carried from 2018 into 2019, leaving you with $0 of excess and $0 of penalty.
