Let's not loose sight of the fact, like CJD posted, that we still don't know the cause of the knocking.
I personally would not use this engine until the origin of the knocking sound is found.
No, the self-locking bolts have a normal hex head.
The bearing dimensions are the same for the TR3 and the TR4/4A
You did check the plug on number 4 cylinder for a loose ceramic insulator or electrode, right?
Question, when the knocking sound is occurring and you gun the engine and then snap the throttle closed, does the knocking change to a rattle?
M.