definitely start getting all your attempts at contact in writing. write up a nice clear letter of the facts as you understand them: your original estimate, what it covered, deadlines... then what actually happened and this error-full bill, what days you called them about the bill, and their mysterious response. Give them a short period for response after which state you will be contacting your attorney or filing in small claims court for breach of contract for the unfinished work and incorrect bill.
I would file a complaint with the BBB if they do not respond within your time period.
sorry this has happened to you.... finding reputable companies with good workers is very hard. it sounds like you did the right things.
did I say one project at a time?