When there exists a discrepancy in the Ordinance, the law favors the Homeowner.
Also, as I stated before, check the revision to see if anything was added.
If they added (d) and you had them prior to the enactment of the new Ordinance, you are grandfathered.
PS (I am a Zoning Officer in PA)
Personally, I would let them cite you, and go to a hearing.
That being said, you are talking a risk that the court will go against you and you will have to pay the fine. I think the risk is very small and unlikely, but it exists.
The courts usually will give you time to correct, without imposing the fine, especially if they see you have a decent argument and you were not trying to ignore the order. Its clear you have been trying to work it out with the Municipality.
That has been my experience, but I do not want to give you false hopes
You might want to consult a lawyer with Zoning experience. Most will give yo a quick consult very inexpensively.