I bought a 2002 Mazda Protege 5 and the engine was knocking pretty good. The dealer said there was a broken rod or something in the head. Put a new head on it with all new timing components. Spun the crank, and everything spun fine, and no scarring on the sleves or piston heads. I spun the camshafts in the old head and nothing appeared to be broken. Put it all back together, started it back up and the same sound. Is there a sensor or and adjustment to be made? It sounds like the timing is off, but I have triple checked all of the marks.
Uhh there are no rods in the head. That dealer has a loose rod in his head maybe.
The crank, rods and pistons are all in the bottom end of the engine.
What it likely is is either a broken piston skirt or a spun rod bearing.
Spun crank bearings are rare and sound deep.
A spun rod bearing can be fairly quiet on idle depending how bad it is worn out, but it will be really loud on acceleration. Piston slap from a broken skirt can be pretty loud too but it mostly sounds like diesel rattle only a bit less. Some have described it as a loud pinging sound like detonation.
Drain the oil and check for metal debri. If you can tilt the vehicle a bit for the oil to drain more towards the drain hole that could help. Then look for metal pieces and judge their size. There should be NO glitter whatsoever in engine oil, or any kind of debri. Now a rear end or transmission is different. Those always have a little metalic sheen to them.
Best of luck.
You might need to pull off the oil pan and check the connecting rods
Fig. Knock sensor removal and installation-Mazda 3 
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possibly could be the harmonick balance
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