I am assuming the stud that is too short is the original equipment stud on the vehicle axle flange. Napa (and others I am sure) has a chart that shows the original equipment stud's dimensions so you could find a longer stud with the same diameter and thread pitch dimensions in the catalogue. also, some of these adapter/spacer suppliers used to have a "necked down" longer lug nut that would fit into a machined mounting hole in the adapter. these would allow the nut to fully contact the original stud. maybe check the supplier if these are available or required. if it is a stud on the adapter/spacer then contact the supplier for sure.
see link below for an example of the "necked down" lug nut.
https://www.alibaba.com/product-deta...539784951.html