I leveled, then shored up the Mustang with 2"x6" and shims when I cut out the structural cowl. I was worried about the same thing. Worked perfectly, the new cowl panel was exactly centered, calipers showed less than .25 mm from perfect. (In other words, better than the mass-produced factory achieved.)
Talk to camarojoe, he knows pretty much all the WNY shop guys. Neat little ride man. :tup: