The Lexus afm (electronics from mk3 and LS400 are identicle) is bigger, so the computer tries to compensate the larger amount of air with a larger dose of fuel...causing a bogging or "misfiring" effect.
Its really just the motor is running so rich at idle. You might have fouled out some plugs though. I would check them before anything. I went through 3 sets of plugs in 1000 miles after my rebuild. tuning the car/getting it running right in time.
-Jonathan
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