Only issue with removing the EGR system is the CEL that will be given. Its done to eliminate some of the BS vacuum lines that are under the hood and clean some of the air going into the intake tract. There are block off plates available online for the deleted EGR system, or if you have the means, you can make your own.
LS1 5.7, T-56 6-speed trans, DGR Fabrication motor mounts, PSI Conversion LSx harness, F-body 3'' aluminum driveshaft, Tuned By Frost PCM, Mishimoto Supra Radiator/Shroud/Fans, QuickCar fused switch panel, Full custom Speedhut dash cluster/gauge setup, gutted and caged. Coming soon, Borg Warner S475, 5'' downpipe, water/meth injection, 90+lb/hr Injector clinic injectors, Brute Speed blower cam, and more