Nice work. I found with my repop inners similar results. I found the best for me was 2 bolts first in front core(left loose), then the large upper bolt to cab(left loose), then install outer fender loose, then attach inner to outer starting with the 2 bolts at top of inner fender(vertical bolts). Those 2 vertical bolt holes where what was really off and made everything suck so they got the die grinder a couple times. Then after that once I had them installed I found the inner fenders stuck out too much from outer fender. Had to trim(grind) that lip down to match outer fender.
Ton of work I know, and I bet they are different for every truck. But I must say, looks like you did the best fix your way, its the right way to fix these things for the best fit.