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As long as the noise goes away when the engine is warm, you are still OK. Sounds like the valve clearances may need to be adjusted. The 1ZZ-FE engine is pretty noise, even if running well, my 2002 sounds like an older diesel truck for the first 5 minutes or so before the engine warms up and then is is fine. Been doing that since 90K miles, I have almost 180K miles on it now - runs very well, doesn't consume oil, all original sensors, and returns ~34MPG+ HWY mileage consistently.
Worn timing chain guides and worn timing chain tensioner can also attribute to alot of the tapping noises from the valvetrain. If you are feeling adventurous - you can tear down the timing cover and check the chain for stretch and if the cam gears/timing chain guides are worn.
You can try different brand of motor oil or even switch to a high mileage oil. Many have seal swellers that help condition the rubber o-rings and gaskets. They also tend to quiet down the sound of the motor. Some semi-synthetics and full synthetics are the same way.
Good example is Pennzoil Platinum vs Mobil 1. Both yield very good UOA (Used Oil Analysis) results, but PP makes the engine seem much quieter. The downside is I dropped about 5-10% in overall fuel economy. Viscosity wise, the two oils are close, but the PP tended to stay in grade or even thicken up toward the end of the oil change interval. M1 tends to run a little thinner anyways, and can shear down significantly depending on the conditions.
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2002 Corolla S, 1.8L 1ZZ-FE VVT-i
2003 Matrix XRS, 1.8L 2ZZ-GE, VVTL-i (RIP)
2009 Matrix XRS, 2.4L 2AZ-FE VVT-i
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