exactly... Big Chevy, I replaced all the cowl and parts of the fenders. I had no holes at all that lined up. I bought a hand full of clamps and used a few sets of vise grips to hold the fender in place. Then I mocked up the whole front end tweakin, pushin and pullin until I was happy with the fit (hood and all to make sure it would open and close right. Once that was acheived I marked the fenders and cowls. I was able to dril at least one hole in each side with the fenders on. Then took it all apart and drilled the rest of the holes and put it back together.
The lines came out great.
Don't drill the holes too small you will need to have a little play
Rich