The center brace bolts directly to the core support. Looks likes someone forgot to unbolt it before and twisted it up pretty good or something like that.
The outer brackets go on the ribs with those two cage nuts, with the nut on the bracket going up to be bolted to the upper filler panel.
I’m with Eric on this, to me it’s suspect that the clutch gets changed and noise begins. These trucks tend to use a lot of fasteners that are pretty close in length, say 3/8x1” and 3/8x1 1/4” and it can be easy to put one in the wrong place, or replace a bolt with a new one that is “close” in...