Well, just because you pass gateway doesn't mean you necessarily pass nondiscrimination. Gateway is just the price of admission.
I agree that you don't have to do prorated limits if you use the full plan year.
I don't think the Form 5500 statue of limitations (SOL) is the guiding SOL.
You owe an excise tax on the over contributions for all those years and that is done by filing a Form 5330. Since it doesn't sound like you ever filed any of those has any SOL started? It would seem like the relevant SOL would start with that form not the 5500.
I think you owe for all the years back to 2007. Willing to be told I am wrong as I can't think of any cite to say I am correct but I don't see the 5500 SOL is being applicable.
What is true since that excise tax is cumulative whatever years you do pay will be effected by those older prior year.
I will add if you can show that this was an innocent error and once discovered was fixed quickly the penalties for late filing and late payment are often times waived by the IRS if you ask. I have had much success getting late Form 5330 penalties waived over the years. This leave the client only paying the tax and interest. The IRS never waives interest.