I haven't read through this entire thread yet, but AutoSpeed has some articles explaining how modern EGR systems can be used to increase fuel economy.
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I've actually installed the system mentioned in the AutoSpeed article in my Honda Accord, and seen the MPG of my car jump between 6 and 10% depending on whether I'm driving in the city or on the highway. I set up a potentiometer that is wired so as to add resistance to the lift sensor on the EGR system, which fools the computer into thinking that the EGR is closed more than it actually is. I've also wired in a switch to allow me to go between the stock EGR opening and the modified values. On the Honda ECU, the computer is set to apply EGR at light throttle loads (<50% or so), but not at idle speeds (to prevent the engine from stalling). I'm not sure about Toyota or other manufacturer's systems, but this means that on the Honda, drivability remains the same, but part throttle cruise fuel economy improves, and the coasting distance with the throttle closed increases.