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What type of noise is it? If you actually think it is the timing chain itself, then it is worth removing the cover and inspecting the chain tensioner which is on the rear side of the head - it's easily visibily and you'll know what it is when you see it. As for the VVT assembly not working i'm pretty sure you would know from a CEL. The OCV that controls the VVT actuator has quite a few codes associated with it. Don't rule it out though.
As for the oil consumption problem, they probably honed the cylinder walls which is something you're not supposed to do for a 2zz motor because of the liner that is on the cylinder walls. Call the shop that built the engine and see if they honed it (be slick about it and ask them if they honed it rather than saying 'you're not suppoesd to hone it, did you?'). If they did, you're going to be drinking oil forever.
Did you have an oil consumption problem before this rebuild?
As for the oil consumption problem, they probably honed the cylinder walls which is something you're not supposed to do for a 2zz motor because of the liner that is on the cylinder walls. Call the shop that built the engine and see if they honed it (be slick about it and ask them if they honed it rather than saying 'you're not suppoesd to hone it, did you?'). If they did, you're going to be drinking oil forever.
Did you have an oil consumption problem before this rebuild?