i bet its just all the tolerances stacking up, these cars where not made perfect in the first place and i gues it only gets worse after 30+ years of abuse..
and trust me stock replacement enginemounts are nowhere near perfect, i had a slight clearence problem with my tti headers also but on a smallblock abody when i put in new engine mounts and gues what, i put in my old original mounts and it made a whole world of diference...