I think I understand now...I was thinking about the motor mount as in the round poly bushing that the center bolt runs through, but now I think you mean the actual metal mount bolted to the frame, right? Shimming underneath that part? That makes sense, I think. Would I have to smim both sides equally to avoid some other issues, or just the driver's side a bit?
This, of course, only applies if I get headers with fitment problems.