Well, having the dpfe sensor should not cause an issue, having the egr vac.regulator plugged in electrically and having the vac.lines plugged in could cause issues. I would leave them both unplugged. Is your egr valve completely gone or do you have an egr block off plate? I would think that an egr block off plate after the valve would be the way to go with that- this way everything could still be hooked up- you would just have no egr flow when the pcm commands it. I have seen egr sys disabled, my thought on egr is that it is doing nothing acceleration (when your making the most power) and it does not cause any lose in performance when working properly.