I am not surprised at what happened. HCl is a bad thing to put on stainless steel. I hear about this happening all the time. First, you need to try to neutralize any Cl residues with a good alkaline material, if this has not been done. Then, depending on the degree of damage, you need to repassivate the surface with a good passivation product. If the pits are too bad you may have to take more drastic action, like electropolishing with a wand or something. Sometimes this is the only way to get the steel back to its original corrosion resistant state. Can you get to all of the surfaces?