I have no idea about the 2JZ-GE, but this stuff applies to most engines.
It must be getting extra air past the throttle body causing it to idle high.
Is something preventing the throttle butterfly from closing all the way?
Are there any pipes coming off the plenum that are leaking, or connected up wrong?
It must have an idle control valve, or something, so the ECU can control the idle. If the crank case breather pipes go back into the intake, the idle control valve could be full of carbon build up making it stick. Can you take it off to look? You can clean inside it with carb cleaner.
Can't think of anything else.