Is $86,000 to install a standing seam metal roof a fair price?

I'm getting a standing seam metal roof put on my 1860 Victorian Italianate house, which has a lot of decorative trim and crown molded fascia boards along the roof line that I specifically discussed preserving. The project is turning into a nightmare, dragging into week 4 when it was originally quoted for 1-2 weeks. I've had several problems: the workmen smoke and leave cigarette butts all over the property, they tore off nearly all of the crown molding which my carpenter believes was salvageable, they damaged multiple window screens by tossing debris, and the gutters with downspouts are still not installed. The roofing company is now asking me to pay an additional $4,000 to replace the crown molding they removed, which I believe they should cover. I feel like I'm being fleeced and am considering refusing the final payment until these issues are resolved.