I worked for/as a stair builder for a while a long time ago. Hardest job I ever had in my life. I would assemble them in the morning and deliver them in the afternoon by myself, off loading them from a flatbed truck and getting them into the building. I got paid for eight hours at minimum wage but usually worked 12 or more every day………. Getting fired from that job, the only job I was ever fired from, was one of the best things that ever happened to me.

The fact that they got the rise and run wrong leaving you with the wrong head clearance would be a code violation, I would think, and enough reason to have the stairs replaced.

The risers are a joke and I would withhold payment until corrected.