I am a Fire Inspector and plan reviewer and we work closely with the building department. What you are going through and what was discovered is a normal day for us. As suggested before, be upfront and don't make excuses or blame others. Be willing to cooperate and be compliant. This will go along way in helping YOU. If they see you are willing they may be more lenient. An example is maybe instead of opening up walls they get you to get an affidavit from the drywaller etc.
I would not continue to work though, any extra labor or materials you put into the house at this time may be required to be removed and sends up a red flag that there are things your trying to cover up. Why finish a wall that might need to be reopened to inspect? When I am dealing with contractors or un-permitted work, if the contact is cooperative we will just require a double permit fee and then just require you submit plans to make sure everything is compliant.
Do you like dealing with A holes? Be a doosh to me and you will get a stop work order, a fine, be reported to any other department that would issue a fine and so on. I am not " high on power" just don't care to hear excuses why you think you don't have to follow the law. Because the Florida building code and the Florida fire prevention codes are mandated by state statutes which make them legally enforceable.
I have seen the building department pull power, I have seen them void any previous approved permits, when work was performed without a permit they have considered the building a shell and required all new permits for the entire building (this was a commercial building) but that meant everything had to be brought up to the latest code requirements.
With all that said, you won't "get one over on they" and just being honest ( now I am not saying confess to everything you have done) but listen to what they say and be co operative and you may be surprised at the outcome. If you plan on working with these departments in the future you will have built a better relationship for future interactions.
