\6 knocking

Lots of times, there are several causes of knocks. Not the least of which is galled pistons from overheating. That can mimmick a rod knock and fool even the best mechanic. That's why, after going to all of the trouble to pull the engine, it should have been disassembled and diagnosed, instead of guess work. It would have saved you a lot of trouble and you'd have a good running engine instead of the same problem.