Greg,
If you took the area off of the drawings and made accurate calculations from those drawings then you can not be over what you figured unless the drawings were not accurate.
I just got back into wiring new homes and have been tracking everything about them. I can tell you everything about my history for this particular builder, cost per sq ft, labor per sq ft, sq ft per hour etc. When I bid to somebody else I have a good base line from which to estimate. However you have to watch when you get into custom because of expectations. You have to at least look into what the customer is going to expect. Look at what types of lighting and other fixtures are spec'ed. Make sure that the two of you are on the same page.
It sounds like the customer had one set of expectations and you had another. Go back over your contract documents and see what you told them, see what they told you, it may be a misunderstanding or it may be a case of misrepresentation on their part. Either way the sooner you address the problem the sooner it will be resolved, or not, but it won't go away at this point.
Good Luck
FRANK
