Kinda off subject. We did an oil change on a customers car, when she picked it up I was accused of putting a 1000 miles on her car. I explained to was impossible to put 1000 miles on the car in the two hours it was at our shop. My point yes it is tough being a mechanic and or shop owner. It...
Maybe your mechanic will agree to discount a motor swap since he missed the rod knock. Worth asking to apply the labor charge for the timing chain to a motor swap if you do the FZJ80.
With the engine running remove/re-install one spark plug wire at a time. The knock will go away or lessen on the cylinder with the bad rod bearing. If nothing changes probably not a rod.