Boy am I glad I'm not you! But seriously, here's my unsolicited opinion:
I have 4 rules that there are no exceptions to.
1)Never ever ever ever ever bid a custom home by the square foot.
2)Never wire a new house where someone else has installed the service entrance without a detailed written agreement full of disclaimers pertaining to the service size, location, and equipment.
3)Never agree to finish wiring a house someone else started without another long, detailed written agreement full of disclaimers.
4) Never accept a job on someone else's service calculations and electrical lay-out. Not even the architect's.
I don't know what the answer here is for you in this situation. If you just finish the job as is it will probably be your name that is mentioned every time their is a problem and there could be many if the service is inadequate. You could make things right out of your own pocket and count it as an expensive education. It may sting but it will be cheaper in the long run than a bad rep. A lot depends on who you are working for. Is it the homeowner or a GC? I would suggest that you run, don't walk to who ever that may be and do some explaining and negotiating. Good luck.