Mislead by my roofing contractor. How should I handle this?

Insurance covered all but $1000 of my roof replacement. Roofing company agreed to do the job for what insurance paid (+ my $1k). Contractor sold me on a higher grade of shingles than he actually used. He also did not install the shingles to a degree that allowed me to get the higher wind rated warranty (even though he acted like he knew what he needed to do to get this taken care of). Job was just completed, but I have not paid them yet. How should this be handled?