If there's no room left on the bolt holes to move the hinges inward (don't go too far as the door is supposed to be a little proud of the cowl so it doesn't rub when opened), you could enlarge the holes a bit. If that doesn't work, you might try prying the hinge bar outward a bit, which should move the hinge point (forward of the pillar) inward.
Hope you can get it figured out. Fitting doors can be a giant pain.
