It looks to me like the damage was done by using a 3pt backhoe on the tractor. I cannot visualize any way that an implement could have caused the damage. A 3pt should be able to handle any standard implement that it can lift, including surge. But 3pt backhoes are a bastard rig and famous for tearing up the back of tractors. They have their uses, but one has to be very careful not to break the 3pt.
Not sure what I would do to fix the attachment points. But whatever the solution is, I think that it will involve putting permanent studs into the rear axle housing rather than trying to patch up the original reusable threads there. Think about either either improving the existing threads for permanent studs, or you may have to weld or pin the studs into the axle housing. Each hole will probably take an individual approach, but I think it should be a decent repair and not too hard to do as long as having permanent studs will still allow the replacement 3 pt flange to be fitted up. So the first thing to do is to determine if the flange can be mounted over studs in the axle. That will require either some thought and visualization or maybe even making up some simple studs and see if the 3pt housing can be installed over them. The problem to look for is that sometimes a housing needs a bit of a sideways motion to get it into position, and if that is the case the whole stud idea it may need some re-thinking.
No matter how you do it, I don't think you have a thing to lose by trying to mount a replacement new 3pt flange. If you can get it mounted up good and solid I bet it will last.
best of luck, rScotty