Completely turning off EGR

I've got an 02 GT that I've removed the EGR system completely due to changing the intake manifold. When I was just using the handheld tuner I could just select EGR off and never got a CEL. I've since cammed and procharged it and I'm writing my own tunes with SCTs Advantage III, but I can't seem to find what turns off the EGR self test system. I've run through everything and turned off everything with EGR in the name but without fail the CEL comes on for P1000 and P1401 after about 150 miles or so.

Anyone know what the special combination of things to turn off is to completely disable the EGR system?
 
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They fixed it in the SCT software where you cant turn the codes off now for the egr. I have the same software and used it to tune my stang. The update came out early summer which fixed that due to the EPA now regulating what you can turn off due to environmental concerns. You should have taken the same quiz I did when you bought the software that explained it. There is no support for our software which sucks. Just add me since you and I both use the same tuning software. You can also email me your information if you'd like to bounce things off each other. Just send me a message and I'll provide my email and number. I'm located in ohio.