If you have a non-EGR EEC (probably needs to be same transmission and as close to your year) I would install that. Otherwise, just keep your EEC and keep the small black transducer box plugged in under the hood.
Without actually having the EGR doing it's job, your car will run slightly leaner under part throttle (because you just replaced the recirculating exhaust gas with extra air from the filter, however the EEC is still commanding the same amount of fuel from before).
WOT should be the same with or without EGR since it is shut off at WOT. Anyway, my point, the non EGR EEC should provide more fuel at part throttle so you won't be on the lean side. But either route will work.
Micah