You probably need some longer bolts and spacers.

Apart from that, what I can see from your photo is you sit the cooler flush against that metal beam, and the piping on the RHS of the cooler isn't sitting level with the core outlet, where as the LHS piping is.

The cooler may be in the right spot, its just that your piping is not installed properly, or wasn't bent into shape properly in manufacture.

Undo the clamps for the RHS piping and jig them around to see if you can get the core outlet to sit flush with the inlet of the piping. If not, its going to be a cut and shut job.

"Genuine" HDR cooler is the same as every other Chinese intercooler setup, no guarantee they'll fit properly.