Hrm... Well, if the Pioneer head unit DOES ignore the remote (or most of it, i'd guess it would react to the Source button), then you could just make one of the buttons on the remote a Shift Lock button, so that when pressed, subsequent button presses on the remote will send commands for the empeg. In an "unshifted" state, it would just be seen by the Pioneer. So all of your IR Translate stuff would be accompanied by the .S shift modifier.