You are "stepping into a hornet's nest" - the thing I am worried for you about is losing your spot on the wait list to rent out your unit short term legitimately.
This is a legal argument, and while presentation is important (you don't want to appear arrogant about your violation), the way in which your presentation goes is going to be much more dependent on the legal issues than the way you appear.
I understand that customers don't come here to be told "go hire a lawyer" - but in a situation such as this, the only way to properly ensure you are represented and can address your rights is to have a lawyer represent you.
(Having a lawyer provides a lot of benefits, they will be able to review the law (discussed above), they have experience arguing these matters (also discussed above), they can prepare a more thorough argument to represent you (this is what we do for a living), they represent a 'buffer' between the legislative/regulatory body and you (you don't have to appear and apologize, and start every phrase in a conciliatory fashion - your attorney can represent your case much more forcefully - this is going to be very important if you want to keep your status on the rental list).
I cannot make the decision as to whether or not you wish to hire a lawyer, but I wouldn't go it alone if I were in your shoes (use the business judgment formula I provided above to determine whether or not this is a worthwhile investment, but this is a relatively small investment for legal services (I don't think a lawyer is going to charge you much for doing this)).
As far as what you want to do if you go it alone. Start by researching the law on the application process, and what factors go into losing a spot. See if violations of the rental code can lead to losing your spot on the short term list. See what other disciplinary action can result. Knowing what exactly your legal position is is going to help you focus your legal arguments.