Before doing any 5500 filings, follow @RatherBeGolfing's suggestion to involve an ERISA attorney. Given the long period of time the plan was operating out of compliance, the attorney and TPA together can work with the client to determine if all of the information is available to complete the forms accurately, and is available to apply remedial actions to bring plan into compliance. If the information is incomplete, then the path forward likely will ultimately involve negotiating a resolution with the IRS and DOL.
Sometimes in situations where plans have been out of compliance for many years, the cost and effort try to to reconstruct exactly what should have happened versus what did happen, and then trying to apply the prescribed remedies can be economically fatal to the company. A knowledgeable ERISA attorney may be able to propose another strategy that could be painful but not fatal.
Having a strategy for remediation can help determine when the 5500 filings should be submitted.