Yeah, one of the first things put on is usually a carb or intake and that changed angle is usually a problem when the stock throttle pressure linkage is used. A simple fix would be to add some lengh to the manifold bracket by extending the legs with metal and a wleder.
MK, Once that roof got tweaked, everything changed. I wonder if I know the guy. It's being sold by a Mustang rebuilder and doesn't list the owner.