The problem you have is not a big deal. As Dave Severson pointed out, this is just normal fit-up work. Slot some holes, rotate fender a bit (if you have to) use large flatwashers, and tighten everything a bit at a time so as not to severely "tweak" anything. The splash apron will come out to meet the fender. Some people assemble the entire front and rear fender, splash apron and running board as a unit, then with help of a friend carry it over to the frame and bolt it to the frame and running board supports and body loosly and pull it into final position with the mounting bolts a bit at a time.