Hey guys,
So, I went back to the tire shop, and informed them of my findings. They had a guy come right out with a torque wrench. He removed the “what I thought was a cross threaded” lug nut. However, come to find out, the stud is fine, and the 1 lug nut is longer than the other 4 (hence it stills out further). They all torque to spec, but obviously one of my lugs got mixed up with someone else.
The tire shop is ordering the correct lug nut for me, but at least for the time being all is ok, including my stud! Thanks for all of your help!