re: Permitting question- we may have unknowingly screwed up

As far as living in the home, you aren't. The issue is you told him about the addition and you want him to consider it in the value. If he mentions it, FHA wants to know about it, because they do not want a new buyer having issues in the future. They just want them to pay the note, not repair the house. On a refi, not a huge deal unless you need it for value. However, your deal with this lender is pretty well shot unless he doesn't mention it. Some lenders may even check permits. It really depends on what company and type of loan you want.