Accelo, I checked my backup and taillight openings and I didn't have the same issue you are having. The holes in mine were good and I should be ok. The only issue I did have was the backup light bucket opening was tight in the bottom corners. I did open them up a little with the body hammer but I will need to tape them during assembly to make I don't chip them.
I also installed the LH wheel well. The wheel well is from Auto Metal Direct and is 0.052" thick. Fitup was good once I put the wheel well to bedside bolts on first and snugged them up. THEN I installed the wheel well to bed bolts. For the bed bolts I put them in at what ever angle they went in at. I then did the two corner ones first just to pull the wheel well down far enough so that I could get the two flat washers, lock washer and nut on all the other bolts. I then started in the center running the bolts down starting the center and working my way out. The only two holes that did not align up were in the two corners where you go though three layers of steel. Once I opened up those holes a bit everything was fine. The bedside to bed was good with no major tweaking.
NOTE: This is a two person if not a three person.
Next up, figure out my fuel filler routing and placement and the RH bedside.
