Swap 2000 4.6 3v with a 2007 4.6 3v

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Physically speaking, the bellhousing and motor mounts are the same, so it would bolt up to your car/transmission, and it doesn't appear to be any wider than the 2000's 2V, so I doubt clearance would be an issue.

The challenge will come with the electronics and etc. Electronic throttle, different exhaust ports, cam phasing and etc are all specific to the 3V and would need to be addressed. They can be overcome, and there apparently used to be a kit to adapt a Cobra throttle body and 2V exhaust to it, but the company that makes it doesn't seem to be around.

Whether or not it's worth the effort depends on your goals; for what you'll likely spend on a 3V, you could probably make more power on the 2V, or even swap in a 4V.