You can't run an aftermarket uppipe with the egr in place. So I would say, save your cash until you can swing the egr delete tube, manifolds and uppipes and do them all together.
Just an update on the truck... Its halfway done I'd say.. Expecting to start it up friday when the ECM from duramaxtuner shows up! I'm getting excited.. I talked on the phone with him for a while he seemed quite confident that the motor should hold together pretty good at the 600-650 range..