Mine fit the same way. I built an alignment jig off of the original cowl and fit the new one in using the jig. I had big gaps like that as well. Once I got it tacked in several places, I just took a hammer to those edges and tried to hammer them down as best that I could so that I could weld it to the supporting structure.
Think of it like a trim carpenter would...nail it and caulk it!
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