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From memory, the stock holes are covered in either gromets or tape (the tape is painted over.) They have to come out so you can set the bolt plate. The front brackets have only two holes, and flange with two holes should sit flush against the body and Z inward toward the frame. The rears have two sets of two holes, each application uses a different set.
I think one set of the brackets can be swapped to get them to fit right. It's been a while since I had this problem, but I had a customer going through the same thing. I got under it and it fit in just a few minutes. Try moving the brackets around.
Rezvani's Latest Post-Apocalyptic Monster Is a Ford F-150 Raptor Underneath
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