On my 66 short stepside I used rope style insulation. It’s like play dough . Comes in strips about the size of a pencil. I put two strips above the bolt holes & two below& just let it fill in any gaps as you tighten the bolts. It’s inexpensive & any hardware store will sell it. My bedsides & fenders were painted prior to install. Stuffs been around forever. When I worked as a flat rate mechanic in a Lincoln/Mercury dealership in the mid 60’s we used it then to seal up leaks in body seam joints or whatever.
