you have to keep the vac line that goes from the black and white check valve to the all black check valve with three ports thats against the firewall . you need that vacuum source to operate the ventilation system doors for a/c heat and defrost , and for cruise if you have cruise.
you can remove and plug the hose to the solenoid at the Tee and remove the hose to the egr valve and then remove the solenoid but it might set a code or SES light depending on your chip , should be ok with the TT chip , you could remove the egr valve and cover it with a blockoff plate from MArk Huefman .
only do this if your vehicle is exempt from state emmissions
if you arent exempt youll need the egr to function and depending on how good they are youll need it for visual . if it worked before the TT chip a simple change of the chip to an emmision chip or a stock chip if you still have stock injectors may get you to pass . otherwise youll have to reinstall the egr components when you go for emmisions and hope you dont get spot checked between then .