In your photo, it looks like you are lining up the ends of the bed strips with the ends of the angle strips. The angle should be offset to the rear about 7/8" or so. It sits on top of the rear sill at the back and does not reach the front panel so not to interfere with the front panel bolt flange. That should make the cross sills line up with their corresponding holes in the angle. The angle does not just bolt to wood only. It is a critical structural member of the bed assembly and needs to be bolted to the cross sills and rear sill.
Mar-Ktech
