Sounds like you need to follow the expensive route.
I recently went through the same issue with my last home, which I sold last year.
I lived in the center of town on a small corner lot , in the 100year flood zone, with a small stream in the back yard.
I had no choice but to remove my old garage first, then see if I could get through all the local Gov. agencies before I could even draw a new plan. Kind of a catch 22.
I wanted it to go through to improve the property, so I spent $2500 dollars to get it all approved.
It sounds like you need to have a local company who knows the system help you draw some plans.
It sounds like you already have a pretty good handle on the issues, but I can see you wanting to save some money.
I just wish I had some better advice.