Far be it from me to throw stones at this juncture, but this is why it is really important to tack weld, or better yet, use small self-tapping screws to hold the new cowl panels in place, then install the hold and adjust it to make sure that your cowl panels are right for a good hood fit. If it doesn't fit, in will be easy enough to make adjustments to cowl panels to make it right.
I only bring this up now in order for the next guy to have a chance to read this and avoid this kind of problem on their build.
