I did my own 15 years ago - my town (Ferndale) had a "what you need to give us to support your application for a building permit" kit that was helpful. Mine was also non-conforming, so I had to apply for a variance from the building codes. I felt like a fish out of water when we started, but everyone from the building office to the inspectors to the city planning commission were all helpful and very understanding. I also had the advantage of some basic drafting in HS, a couple of years in commercial property management and a handful of prior (unpermitted) projects, so it wasn't all brand new to me.
Good luck, and make sure after you figure out your budget you add 38% for all of the stuff you didn't plan for.
Paul - 2005 Wrangler Unlimited