Lower Torque Box Reinforcements - holes don't line up

[MN_Stang]

I went to install my lower torque box reinforcements last night and the LCA bolt hole on the frame and on the reinforcements don't line up (see pics). The photos here are of the worse side, but both were off a bit. Since the top is just the thin floor pan, can I just pound upward on it until the difference is made up or is that a bad idea for some reason (that portion of floor pan may have warped a little bit from the heat I had to apply to the rusty LCA bolts)? It seems like elongating the holes on the reinforcements would defeat their purpose.