Daddy-O
Thanks for the Bing notation.
My note being 40ft was based on the 3 house stories plus additional cliff outside back by 6' going down another 15' The tree coverage behind the house is below the roof line of the view blue line notes base, magenta notes over all and the red shows window removed and door installed.
GH,
In NJ the state requires a permit for basic repairs even on roofs, unless you replace just a few blown off shingles. I did not mention the stairs or landing because that is inside work and no way to check that out.
As for cutting in the doors to replace windows, access at this point is access.
The simple fact you can get on the roof and it has now been converted to a deck from a roof should be an issue and I don't buy the no permit required.
Here is a question for you what are the design loads required for a roof on 2 degrees and an exterior deck or floor?
Also, I am not sure were you are but skylights in the middle of decks in NJ require guards blocking them if the base is not more than 30" above the deck. Not sure of the code section, but required here.
I tried to keep the guard issue basic, for ease.
As for turning it in, called another AHJ who knows that official and they passed on the information already.