He'll likely have to remove the bumper to spread the rails apart to get the new crossmember in. I used a high lift jack to spread them apart. I didnt take much force. He should be fine. Like you said the rivet holes should square the frame. It is a high flex area, the frame rails move all...
https://forum.ih8mud.com/threads/fj40-cross-member.1280730/
I'd probably use the one you have if its not cut up or not structuraly compromised. Just remove the rivets and clean it up and install it.
The PO hacked in a sag box on one of my 40's and had to deal with the same thing. I tried patching it a few times. Eventually I replaced the whole crossmember and went to scout steering. That portion of the frame is a high flex area. Even removing the box and patching the crossmember...