I've personally had experience with two of the three "bad" engine issues. They both have distinctly different sounds when running.
Click on the links below and determine which one yours sounds like most.
Hope this helps.
1. Timing Belt Tensioner (frequency of clacks is higher than rod knock)
2. Rod Knock
3. Cylinder Head issues (not sure on this one... hope not to find out either)
I just read something on Youtube that makes perfect sense and is worth sharing:
"Joseph Murphy 1 year ago
The best way to trace engine noises is to see if the sound is in time with the crankshaft or the camshaft. The camshaft is twice as fast as the crank. If it's timed to the crank pull the motor."
JIM