The clerk at court is not allowed to, nor should she / he give legal advice, such as the effect of the minister's failure to sign the certificate. There are a number on facts that would be relevant. Did you have a marriage license in 1989? Did both of you believe that you were actually married after the ceremony? Etc. You need to talk with an experienced family law attorney to assist you. You can consult with a lawyer about your question for little or no cost through a lawyer referral service in your area. You can find your nearest lawyer referral service by clicking on the link below.
If you found this response helpful, please let me know by clicking the "Mark as Helpful" button at the bottom of this response. Thank you. Mr. Richardson practices in San Mateo and Santa Clara Counties, and concentrates in non-adversarial dispute resolution as a mediator and collaborative lawyer. The California State Bar Board of Legal Specialization certifies Mr. Richardson as a specialist in California Family Law. He offers no comments or advice with respect to the laws of any state or jurisdiction other than California. The above answer is a general explanation of legal rights and procedures. Mr. Richardson is not your lawyer unless and until you and he have personally met together. This post does not constitute legal advice, and no lawyer client relationship results.
Based on the limited facts you stated, you're likely married. You said the marriage cert was recorded with the county. A simple technicality based on the mistake of the minister not signing the marriage cert is not reason alone to undo your marriage.
You also aid that you were "legally separated." Do you mean that you filed a petition for legal separation and obtained a judgment of separation from the court? If so, then at that time, you've essentially waived any claim that your marriage was not valid due to the aforementioned technicality.
I'd suggest that you hire a local family law lawyer and proceed with a divorce action, rather than waste money or more time on this issue. It will likely be fruitless.