Not All Is Lost For A Non Not-For-Profit
First I am going to intentionally ignore the State issue regarding the failure to file, and be recognized, as a NPO (Non Profit Organization).
Instead I am going to focus directly on IRS Publication 557.
An organization may file an application, Form 1023, after the 27-month deadline may be recognized as NPO. One may also request the NPO start effectively back to when one intended it to start by completing Schedule E, Form 1023, and checking the Yes box in Question 5 of that schedule.
This is important; one should prepare a good narrative, along with any documental reason(s) for not filing Form 1023 until now. The IRS may approve the request if the NPO had a valid reason, and operated in "good faith." I would also recommend a section where one could show that the US Government would not be adversely affected by the IRS granting such a request.
In my opinion you would be best to file Form 1023 and your documented reasons before the IRS finds out. By way of example, only as a hypothetical; if the IRS were to audit one of the people who donated to your firm. A quick check would reveal that you were not registered nor approved as a NPO.
Obviously there is more work that needs to be done and my advice to you is to get this going AS SOON AS POSSIBLE. I would also recommend that you reference IRS Publication 557.
Good luck and best regards,
Huntington Beach, CA