I'd look at the trans crossmember bushings (could be trashed rubber or the actual crossmember, the metal around the bushings in my 86 GT rusted out pretty bad) and the engine mounts. We just installed a set of BBK equal lengths in my friends (my old car) 86, they fit tight and rub the steering shaft and hit the frame on the passenger side. His motor mounts are pretty smoked, anthough the headers could be made to fit slightly better

. I'd also go around and make sure any bolts/mounts are tight too.