I had a friend (an attorney) who told me years ago to not put a "Beware of Dog" sign in the yard. Said if a dog ever bit some one and they proceeded with legal action that sign indicates you know the dog will bite and could lead to negative outcome.
You mentioned the pump guy used the wrong bolt. What bolt are you referring to? Wouldn't the PTO shaft be attached to the tractor and locked on with the setup there? The other end was bolted to the pump? I'm unclear how the pump was attached to the tractor by this "too small" of a bolt.
So the PTO shaft did not break, it got pulled apart? That shaft dancing around there uncontrolled at 540RPM... what does the back of the tractor and the attached shaft look like?
Yes, I want to see the configuration of the ditch that has/had you stumped. Show us, at least, a view from one end so we see the trees and other obstacles.
If I were doing the JB repair I would take a 16P nail and bend the end 90 deg about half inch from the point. Use that to scrape the crack just to clean it out a bit. Then when applying the JB have a piece of duct tape ready to put over the whole thing. This keeps the JB from flowing out/down...
Do you have any pressure with the bucket on the cylinder end you are trying to grease? Move the joystick in all directions to make sure the bucket is setting on the ground without any pressure on that joint, the try greasing again.
How long has it been since last greased? Removing the pin...