An inch of error hardly seems acceptable for a what's supposed to be a premium product. Do the instructions address this modification, or did you discover it on your own? I'm no fan of body lifts. Expect the glass body to set same as OEM steel body and not have to rework other items.
Also, looking for OEM rubber mounts. The urethane mounts I've seen are too stiff for a glass body. Need to flex easily so minimal stress on glass. Have seen vibration from unbalanced tires put cracks in a steel body.