Why would you want to get rid of the EGR? It increases fuel mileage and allows the computer to lead in more timing when allowing flow. It doesn't allow any flow during WOT conditions, thus has no effect on peak power or torque. Unless you are running long tubes and can't physically make the EGR work without a lot of additional expense, then put it back on.
As for your problem... did you put silicon or any kind of gasket on the plate? Could be a vacuum leak. Or maybe you wiggled some nearby wires. Did you disable the EGR in the tune yet?