rfieldbuilds,
What's the anchor rod diameter? What size holes are in the column base plates? I'm asking because base plate holes are now recommended to be bigger than they used to be. For example, for a 3/4" rod, the hole size used to be 1 1/16", but now it's 1 5/16". Holes for a 1" rod used to be 1 1/2", but now it's 1 13/16". I don't know how much the anchor rods are off, but I was just thinking that if the old hole sizes were used rather than the newer hole sizes, that might be the problem. If the anchor rods were not that bad off, maybe they would have worked with the larger holes in the base plate. In my experience, it's not likely that the anchor rods were set out of plumb. COSP doesn't provide detail about anchor rod plumbness. It only states that anchor rods shall be set with their longitudinal axis perpendicular to the theoretical bearing surface. All the tolerances referenced in "Section 7, Erection' are based on the larger hole sizes in the base plates, which can be found in Table C-J9.1, on page 16.1.355. If more restrictive tolerances are needed due to special conditions, this is supposed to be noted in the contract documents.
I will say that there are a lot of fabricators out there who still use the smaller hole diameters. For example, I'm referring to those who don't have the capabilities to plasma cut base plates with holes. Instead, they track torch a 16 x 16 x 3/4" base plate, and punch the old 1 1/16" holes for 3/4" anchor rods, rather than track torching the same base plate and drilling the new 1 5/16" holes that are suggested for 3/4" anchor rods, because they don't have the capacity to punch 1 5/16" holes. It's more labor intensive to drill vs punch, so the smaller diameter holes are used.