I wouldn't worry about your modifications affecting your warrenty. They can only void the warrenty if your mods directly affect the area of concern. In other words if you add a lift and then want the springs replaced under warrenty. Or put a dual T-case in and want the factory T-case replaced under warrenty.

The first thing you need to do is take into a dealer and have them look at it. Make sure they document it and put down your problem on a receipt or something. You want evidence that you took it to Toyota and complained about the problem. Even better if the dealership acknowledges the problem. Make sure they put it in writing. YOu may need this later if you have to fight with Toyota. If one dealer says there is no problem or says they can't do anythign about it, go to another and then if you have to, another. Then call Toyota and talk to them directly.

Hopefully, you have a "factory" extended warrenty. Those are really only ones worth having.

I think the issue is related to later model 3RZs built around 2001 and 2002 and it may only be a few motors as opposed to a wide spread problem like the 3.0 V-6 headgasket issue. I only say this, because those are the only ones that I personally have heard about with a loud knocking noise.

You can also them that you know of a 3RZ being replaced at Mac Toyota, in McMinnville, Oregon, under warrenty for a knocking noise. Just in case they need to hear of a precident.

Good luck.