question about gt40 and egr????

The later models of the explorer/GT 40 intake did not have the EGR passages in the upper manifold. They used an external EGR source from one of the exhaust manifolds. See http://forums.stangnet.com/showthread.php?t=551505 for the full story.

To properly emininate the EGR, you need a custom tune to shut off the EGR functions in the computer.

Not really. jrichker can better answer this but the computer advances the timing at part throttle which increases gas mileage. In order to do this it needs exhaust gasses to keep the engine from pinging. If you put a simulator in there instead of a functioning EGR system then the computer will advance the timing anyway and that can lead to engine damage.

I have read that simply disconnecting the EGR from the wiring harness will send a fault to the computer and it will not advance the timing.