Just because the factory fenders fit does not mean that new fenders are going to fit exactly the same.Go buy new core support mounts, install them loose and get all of the fender bolts in while they are still loose. Use shims to align the fenders. It takes some doing to get it right, it is not just unbolt and install new parts. It takes practirce and Patience to align body panels.
Another thing, the top flange of the fender that sits on top of the core support might have to be bent up or down to get the lower bolts to align.