In my experience the hood to cowl gap has no relationship to your fenders. However it does seem to me all 3 bolts are needed. There is a lot of force associated with the hood (the weight), the spring bars, etc and hinge pieces have been known to move a bit if everything isn't tight. Have you tried (and you will need a helper) unhooking the spring loaded pieces and setting the hood down? First get the missing bolt you need, install it with a washer and lock washer and then adjust the hinges as needed and tighten all 6 bolts. Then holding the hood up, remove the two spring bars carefully and lower the hood gently. Raise and lower it a few times (it will not be as easy when the spring bars are not connected) and see if the gap increases. If it does, let's see if the pivot spots where the two short bars connect to your hinges are okay.
