I have replaced all cowls and floors in my truck and last week I fitted the fenders. Surprise, surprise, everything lined up within an 1/8" of an inch. I chose to cut/fit my cowls below the factory break line using the fender curve in the cowl as the cut line. I believe by not digging into the line (leaded factory joint) it kept things in better alignment. The other benefit is I wanted to retain my original driver side cowl vent and none of the full replacement panels provided this option. May not work for everybody but in working one side at a time I didn't brace the door frames or cab I cut my way in and welded my way out.
http://community.webshots.com/photo/2048522030102454676WUrrxJ
http://community.webshots.com/photo/2936584830102454676JgqnnF
http://community.webshots.com/photo/2828427830102454676OVUktD