Interesting, I vaguely remember noticing this when I first picked up my GX a few years ago. After the 35's though I don't think I notice it anymore

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but there isn't anything else.. you have confirmed that swapping the internals you don't get the same result with your 4runner pedal being the only difference. you can take it a step further and meter out difference values of pedal travel vs output for both but I can almost guarantee you won't see a difference. It's all about the arc length of the pedal travel in relation to the arc length that your foot travels to input the same displacement. You have more wasted travel due to geometry on the 4runner pedal vs lexus pedal. You says "push down 1/2" but that doesnt mean that the pedals have both displaced the same exact amount. Your foot just made the same perceptible displacement but it didn't fully translate into the arc length travel equally between the 2 pedals.

I was thinking about this topic when driving my 2004 V8 T4R, the OP said he had to depress his gas pedal around 1/2" to get response from the engine, I tried this numerous times and mine responds almost instantly to very little pedal input, way less than 1/2", I have purchased a Sprint Booster..BUT I have never installed as of yet because I don't seem to have the pedal lag most seem to talked about on the forum.

Cmon OP - post the Lexus part number already.

The part number is 78120 - 60350.

You beat me to it.