From what I can tell, looks like you need shims to adjust the valves. Could be off a bit, but that video is pretty hard to tell what the clacking sound is. There could be a whole bunch of different reasons for it, from rod bearings starting to go to a bent valve, to even having a lot of carbon buildup at the valves or even piston slapping a ring of carbon at the top of its stroke.
I have the worst manual for an '03 tacoma, so its hard to find what I was looking for in it, and I wasn't about to go through the 1,200 separate pdf files to find it! Of course, if you're interested in doing that, I'll send ya the repair manual!
If you already have a manual, check to see how to set the valves, that will tell you what you'll have to do to see if its just valvetrain noise or something more serious.
You can also try isolating the knock by using a stethoscope, or even a long vacuum line stuck to your ear and prod around the the engine to find that noise would work in a pinch!
Edit!
Worked way too long today, thought you said 3RZ and not 3VZE! Still, the valves on the 3VZE use shims to adjust clearance, but I have the manual to check that. If you need the 2 pages from the manual to do it, lemme know and I can email it to you. File is about 1.2mb.
