Sure, it could be something simple... I've seen a loose cam gear cause a tick which resonated down the length of the camshaft making it sound like it was coming from the back of the engine... but, sadly, I wouldn't count on it; it is worth checking for though.
Unless you pulled the cams and removed the shims and buckets you can't tell if you've lost a valve or broke a spring... pulling valve covers is only one fourth of the trip.
I'm not terribly familiar with all of the construction of the 1JZ, so the best I can offer is conventional diagnostic advice; I can't point you to common failure points.
The next thing I would do is: while the engine is running, pull the wires to the coils one at a time to determine if the sound is indeed tied to one specific cylinder and if so which one.
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