How its done
Well after getting no answers here and some playing around this is the solution. Sears sell something called a Handi Cutter. Its like a PVC cutter long set of pliers with a sharp blade about 4 inches long and a plastic plate for the blade to chomp down on. Get one, they are under 20. bucks and make cutting a breeze.
First, using some 1 inch painters tape run a length of tape on the lower depression right on the edge. Now you will have a line that you can follow for applying the molding. Cut some paper about the width of the molding and about 6 inches long. Using this as a template and a ruller mark the angles to be cut for proper fit. Then tape to the molding and cut along the line.
Clean the surface where the molding will be applied with alcohol and allow to dry. Remove the tape (about 1 foot at a time) and carefully place the molding directly below the tape line. When you get close to the end of a panel (or door) strech accross the area to be cut and mark it with a strip of tape, this way you can get the seam straight.
Remember, when applying the molding and the front of the door edge you will need to cut it at a 45 degree angle to allow the molding to slip inside the front fender so not to hit it.
Hopefully this might help someone!