If I'm visualizing your problem correctly (the bottom of the fender is popping out away from the car and creating a lip there), sometimes it helps to work it a step at a time. Leave the bolts on the bottom of the fender loose and line everything up around the cowl the way you want it, then cinch down the bolts at the top of the fender to lock that in. Then you can move to the bottom edge of the fender and position that bottom edge where you want it, then tighten those bolts while you're holding it in position.
If you look at cars from this era closely that are still original and haven't been touched, chances are you'll see that all the panel gaps are a long way from perfect. Its not unusual to have to put everything under a little tension to get it to look the way you want it to.