About 3-5 years ago, I installed OEM (used, but repolished) wheel lip moldings back onto a 1970 barracuda with AMD rear quarter panels installed. we used the original rear lower valance (with exhaust cutouts) and replaced the trunk floor pan. all those panels had to be tweaked a little bit to fit precisely (well, more precise than factory) , but nothing major.
Later, I seem to recall the wheel lip moldings did not initially fit precisely as they did on the original quarters. but then, they were removed and stored about 5 years prior, so it's hard to say if during storage, they underwent some tweakage. With minimal effort, I was able to bend and tweak those moldings so they laid pretty flat and even, PRIOR to applying the screws. we chose to drill pilot holes, once the trim laid flat and looked good.
I may have spent 2 hours dry fitting them, prior to screwing them in. the first one took about twice as long as the last (I started to git gud)
so in your case, an image showing how far out of whack it is, could help us judge if it needs tweaking, or something else is awry. in the end, they may look just fine, even perfect, if you can get them to follow the contour you presently have.
don't mix them up. I think each of the four is a little different. I'm gonna hit the dealer parts book, to confirm. but these were "a package" so I'm uncertain I'll find the part numbers for each part.