I've found every aftermarket part I've ever put on any type of car or truck has needed more than a little massaging to get it to fit. I put an aftermarket 400 hood on a 68 that took two days of molding to get it to 'almost' fit.

Haven't had anything to do with a 69 but my 68 was something like yours in the first pic I could see. The fender mounting flash was about 3/8" above the rad support, there were washers to fill the gap. That was before I took the front off the car. I replaced the rad support and the body mounts, it was the body mounts under the support. Almost looks like your rad support is sitting too low, maybe the body mounts under the rad support are not thick enough, not likely but maybe worth a look? The other body mounts may also be having an effect on the front alignment

These cars weren't exactly lined perfectly when they were new. Door gaps could have been tight at the bottom and wide at the top. the fender is almost three times as long as it is high. Perhaps you may have to widen the gap at the top of the fender at the door, 1/8" more clearance at the top rear will drop the front down 3/8".

I'm anything but a body man, just sort of thinking out loud.