Take th whole system off is the bast thing to do. If you dont , some people leave the vac line that runs to the egr still hooked and and it can make the car idle and act funny. It doesnt happen all the time, but it does happen Take it off completely and make a little plate to bolt on over the big openening, or buy the plate premade on ebay. MAke sure too, that when you do, you close up the hole that will now be open in your exhaust. They make big bolts for it.