Panel Alignment Tips

On my 1969 I have the doors aligned pretty close to perfect. I have my hood aligned to the cowl really nice. The driver side fender will align with the door, the mid line edge and the top edge really nice but the gap is anywhere from over a 1/4" to 3/16" between the hood and the cowl. Is it better to try to set the gap between the hood/cowl fender first and draw the fender in behind the wheel? Seems like I can get close to the gap at the hood/cowl and that throws the top edge and the mid edge off. So can you persuade the bottom of the fender into place after setting the fender top bolts?

Another question. The hood crown at the rear bows higher than the cowl. Has anybody shimmed the cowl to match the hood crown? At peak there is a little over 1/16" difference. Or is that just the way it was built and deal with it?

Well the hood needs to be adjusted first. The height of the hood can easily be adjusted by the hood hinges, Once the hood is adjusted the front fenders are next.

I ended up putting two shims about 17 inches on either side from the outside hood edge under the cowl. It lined up perfectly with the crown in the center of the hood. The hood back corners are both slightly below the cowl and fender.
I messed with the driver side fender some more and ended up getting the gaps within the specs in the Ford manual. It worked best to loosen all the bolts and remove the two that go into the rocker behind the tire. I lifted from bracket the stone guard attaches to and the wheel opening and kinda of pushed back toward the windshield and twisted and then tighened the bolts below the quarter piece and one of the bolts near the middle of the fender. Checked with the hood and made an adjustment near the front to secure the gap at that point. I loosened the mid fender bolt and then had a helper lift on the wheel opening and secured the fender height by tightening the bolt underneath the top rear of the fender that you access with the door open. I then fitted the bottom rear of the fender into place and secured that position. Made a few adjustments and ended up with everything close to 1/8". The top front of the door may have to rotate in toward the window pillar a little but I will deal with that later. I need to adjust the quarter piece a little as well but I will do that when I get the other fender aligned.
Hope this helps - it is a touchy and frustrating process when you do not know what your doing but it will finally come together.