you forgot option four, play dumb, gosh boss that was so over my head i didnt understand a word of it, could we schedule some time to go over it together?
Its friendly, it offers her the opportunity to fix it and you can keep records of your emails back and forth.
the more disagreable you are the shorter your time there will be, she will find a reason to get rid of you, weather you did anything wrong or not.
Simple gifts had some very good advice, protect yourself first, keep your eyes open for another opportunity, we spend far too much time at work for it to be heck ever day!