Woody, I had the same problem. First I made sure that the contour of the outer cowl panel matched the profile of the fender. Then I made the inner to outer match that profile.
Concentrate on making what you will be looking at most, which is the outside, fit well. And if that fit between outer body panels is a relaxed fit, it will save a lot of heartache when it comes time to do the final assembly.
I needed to cut my inner to outer to make it fit, and the kick panel too. It now looks like it did when new and there is no trace of the blood and sweat that it took to get there.
I have always built from the outside in. Others may take a different approach, but that has worked for me.
